If the only thing you touched was the carbs and it has changed that much, then it's the carbs.
If they are the stock CV carbs then you could have a ripped diaphragm or a clogged jet or something else amiss.
However, if you've changed a lot of stuff all at once (adding pod filters and changing exhaust as you stated) and now see these problems, it is a lot harder to know where to look.
I would suggest you check the big things first by doing a compression check with the carbs off. Make sure the valves are adjusted correctly and the mechanical side of things is solid.
It's quick and easy and you can scratch those things off the list of suspects pretty quickly. (and if you do find a problem, getting the carbs right wouldn't fix it anyway)
If the compression check out right, then I'd suggest another full carb disassemble and clean. Yes, you just did it, but you have to know for certain that everything is clean and correct in there.
Another thing to double check is fuel flow. Petcock, gas cap vent, inline filters, needles and floats are all suspect until proven good.
Things that can potentially cause this symptom are many and varied, from incorrect fuel flow, to valves way out or cam out of time, carbs way out of synch, clogged jets, ripped diaphragms, float bowl vents clogged, and the list goes on.
If you can share more information we may be able to help you narrow it down some.
Best of luck!