This reminds me of another recent-ish thread that has some bearing on your questions @Babale
In which my comment was as follows -
If we’re talking about essential freedoms, are we talking about essential freedoms to operate in a liberal democracy? Because those are quite different than those for a oligarchy, dictatorship, or theocratic state.
Or are we talking about what we feel are the essential rights of human freedoms in a moral or civic sense? Or, in a similar but more specific sense, what if we had a functional world government, what we would require as essential freedoms in order to be a part of such of a body (say like a UN Human rights charter but with teeth)?
Personally, the one I would consider the most critical freedom of what we’ve already discussed is @Oredigger77 's ‘pedal franchise’ - the freedom to leave. Of course, from a rights POV that pre-supposes there’s a place you can go more in line with your needs or POV, and that such a place respects your right of entry.
I think your OP is framed a bit better, but falls afoul of some of the same issues - because what we perceive as our rights or freedoms (not the same) are social and legal constructs specific to the societies we live in.
So continuing with your OP, the focus, fairly, is on 2nd Amendment rights. In general, I take the OG SD column on the POV of the founders to be largely correct, in that having just fought against the (arguably) largest military of their time with personally owned weapons, that they did indeed support personally owned weapons, and simultaneously had a deep distrust of a standing professional military.
I -ALSO- support your statement that even if this is the intent of the founders, that we do not live in the same political state and structure that they did, and we have the right and opportunity to alter our governmental and societal structure to better reflect our own wants and desires.
So, back to the questions of your OP.
What are rights for?
IMHO, rights are the minimal legal protections we have determined to enshrine in our body of laws. Different societies/nations/etc will define those rights differently, but that’s another thread. 
Where do they come from?
In a republic or democracy, ideally they come from the people and those they’ve chosen to govern, and would (equally ideally) continue to reflect the wants and needs of those people. In practice, they often come from those individuals or groups that have the influence and funds to make their voices heard. And that leaves out non-representative governments entirely.
A yet more idealistic interpretation would be that of the Declaration of Independence, wherein we felt that certain rights were intrinsic to the human condition. It’s a beautiful piece of work, but not even adhered to fully in the US, much less other nations and cultures, but it’s definitely something to strive for rather than against.
Including the 2nd Amendment
And now is where we get into the weeds. So the second amendment is a right written to (per point 1) protect the rights of persons involved in the social contract of the US constitution to own firearms, at least according to my personal, and currently held position of a wide (but not complete) body of constitutional scholars including members of the SCOTUS past and present.
It comes from the Bill of Rights, which was the first group of supplements to the early constitution to amplify what was a rather bare-bones agreement of what the government was to be, and it specifically addressed point 2 above, where the other founding fathers felt the Constitution as originally written did not address concerns in which the government should be limited in it’s rights to meddle with the citizens - a valid concern considering their feelings on why the split with England was needed.
So, having answered the questions of the OP, let’s dial down to the question inherent in the latter half.
We have, in the US, both the right to gun ownership, as enshrined in law (and yes, many arguments about the scope of regulation and the like, but @Babale specified specific proposals are out of the scope of the thread) as well as a substantial issue of illegal and harmful use of firearms against the population. I am very carefully trying to stay away from the debate on the degree of comparative harm, as it leads us all down the same tired ruts.
The issue becomes then one of law - not necessarily the best moral answer, or the least harmful one, but the one that governs the social compact. Most of Europe, in building their governing documents, has not chosen to enshrine the right to firearm ownership (and that’s putting it mildly) into said foundational documents. Their documents were written for the time and people they were representing as well, most of which were quite different from the position of the American Founding Fathers.
The FF (sick of typing it, sorry), were flawed in their own ways as well, and thankfully put in a method by which the Constitution could be modified to reflect changes as the country’s needs and desires changed as well. But, and here’s the rub, they chose to make it EXTREMELY difficult to make those changes. Not impossible, but difficult.
So we come to where we are now (pages of my typing later) - a substantial portion of the population, justifiably upset with where we are in terms of ongoing gun violence, wish, as is their right to modify the social contract on which the government is based. Another substantial portion of the population, wishes to maintain or expand the right for a host of social, political and historical reasons (and a bunch of dumb reasons as well, but that’s another thread) and is sufficiently broadly based to prevent any changes via the established mechanisms of law.
So, how do we change this? Well, there are options, but they all have consequences.
- Those who wish to change the existing compact educate, plan, organize, and execute political will, until such time as they have a sufficient majority to enact Constitutional change via a new Amendment. The problem is that while this is going on (IMHO, 2+ decades at a minimum and a degree of organization that has been sadly lacking to date), the risks and harm continues, and leaves out concerns that the system is sufficiently stratified to ensure that there never will be sufficient votes to allow it to occur.
- Continue to try to elect representatives to our Legislative Body that can and will follow the ‘well-regulated’ interpretation of the 2nd, to manage to mitigate the harm and risks, while maintaining the essential uses laid out in the OP. Of course, this also gets into the murky issues where out existing two party system loves to negate everything the prior party did when it was in power, and leaves out the issues where as currently aligned, the SCOTUS would likely argue against said interpretation. Another multi-decade or generation fix.
- Fundamentally call for a new constitutional convention, as has occurred in other nations in which the people have lost faith that the government can or will protect the rights and prosperity of the people they represent. But, quite frankly, I suspect if anything, we’d end up worse than we are now. If the federal government allowed such a thing (extremely unlikely, but hey, for debate purposes) we are once again at the mercy of a body of individuals to write a new Constitution, which is going to reflect the special interests and priorities of those writers, no matter how well (or, sadly, ill) intentioned they are.
- Push for better enforcement of the laws we have on the books, or at least, a more even enforcement which applies Federally, rather than on a state-by-state level. This argument is mostly brought up by the pro-gun moderates/quasi-moderates. In that we do indeed have a wide body of laws that should work better than they do to fix these issues. But whether through funding, lack of resources, lack of enforcement, or the competing jurisdictions by county/city/state, never manage to be particularly effective. Which leads us to…
- The unspoken one by most social liberals, and most bloodily anticipated by the fringe (?) right, by Civil War, warm or cold. And this one scares me, but sadly seems to be the way we are headed as our society grows ever more polarized. Since individual states seem determined, with full governmental support, to push their own interpretations of freedom and rights to the forefront (such as the religious right to act only upon their own beliefs), we could well end up with States A-G saying, as a not random example, screw the SCOTUS abortion is allowed here but guns are not, and states H-Z saying screw everyone else, everyone can have all the guns they want but never an abortion. With the federal government being too deadlocked to actually intervene one way or another.
So now that I’ve written a tome, I’ll head back to IMHO territory again. From my personal POV, as a part of the moderate group of gun owners (and I’ve had this discussion with @Babale before in other threads) I respect and exercise this right, but do everything in my power to do so with responsibility, which (again IMHO) is the oft-neglected flip side of having rights. I feel that as they stand, there are a large body of common sense measures that could and should be enacted regarding the safe handling, training, storage and accessibility (purchases, transfers and type) as well as consequences for those who break said measures. But do I see a way to implement them? Not at this time.
Both sides of the political spectrum want freedom, although neither side is particularly good at the responsibility aspect. IMHO, the Conservative side is worse, in that it embraces its rights and freedoms without acknowledging the costs or willingness to accept any responsibility at all for the outcomes (biggest example being abortion, but also climate change and a host of others). My best answer, and the one I think scares Conservatives the most, is that given time (see my earlier thoughts about decades/generations) and accepting that there will be ups and downs, the POV of the needs and habits of a firearms heavy society will change, at which point, we can make the changes via option one or two.
It won’t be fast, it won’t be easy, and it will certainly come after much loss of life. But I believe it will, and I also believe it’s part and parcel of Conservative hatred of things like CRT and scientific liberalism in education. Because they believe it will happen as well.
If and when the time comes (and I doubt I’ll live long enough to see it, but…) I will surrender the firearms I own for destruction or the like, while hopefully being reimbursed a fair-market value for them (which is yet ANOTHER thread). I’ll have some regrets, but I won’t be shedding anyone’s blood over it.