All troubleshooting, electronic or mechanical, starts with what you have in symtoms and then systematically and logically narrows down the potential causes through a form of elimination.
In general, if something worked fine before, then someone "touched it" and it doesn't work fine afterwards, take a look at what was "touched".
In this case the lower was changed, so I'd start there. Functionally speaking, you apparently have no other difficulties/problems. The rifle fires and cycles as it should.
You have three possible areas to investigate at this point (possibly more, depending on what you find as you go along).
1. The ammunition. Regardless of what you THINK about the ammunition, you cannot rule it out at this point. The ammunition you have in hand is NOT physically the SAME ammunition which gave you such tight groupings. Might be made from the same powder, same bullets, same primers, etc., but they are physically not the ones you've shot previously. Any number of issues with the ammunition could cause the groupings to be different. It could also be issues not involving the ammunition itself, per se. Like temperature/weather. Until you test for this, you cannot automatically eliminate it.
2. The lower in combination with the upper. It is, in fact, a different lower.
3. The mechanical interface between the lower and the upper.
4. The operator.
Start with sitting down and shooting some rounds under tightly controlled conditions. Preferably conditions which will exist in future test shootings. (Same ammo batch, same bench set up, same range, same weather, etc.)
After you've established how the rifle shoots under tightly controlled conditions, restore your rifle to its original configuration. This is a go-no go test. If the rifle's accuracy improves, then the issue is very likely NOT to be the ammunition or the operator. (Remember...it's just as important to know where the problem ISN'T as it is to know where the problem IS. Why? Because it narrows down the area where the fault can be found.)
If the rifle's accuracy does NOT improve, then you've established that SOMETHING has changed which affected the overall accuracy of your rifle and you need to sit down and figure out some additional systematic tests to see if you can produce a different result.
Keep in mind that it could be a combination of issues which contribute to this. It could simply be the fit-up (mechanical interface) between the upper and the lower has to be "just so" with either lower to get the accuracy you had before and when you disassembled/reassembled the rifle it is ever so slightly different.
I do a LOT of troubleshooting of instrumentation and control systems. Faults can be a huge range of issues. It could be something the shop screwed up while doing work. It could be that a card/module needs to be reseated. It could be incorrect material used. It could be simple mechanical issues like loose hardware. There are a ton of things. Regardless, successful troubleshooting methodology is ALWAYS the same: It's got to be systematic and logical.
