changed mipide w/cat, still feels clogged...maybe muffler??

apple

i recently changed numerous parts in my car before i left for florida on a road trip from new jersey, altogether i drove a little over 2000 miles. i installed a godwin racing midpipe, new o2 sensors, new coil pack, new wires and plugs,and unrelated stuff like brakes and rotors. then once arriving in florida my master clutch cylinder went. it was all fixed and i got home fine, but the ride still feels like the cat is clogged, and im wondering if the muffler is the trouble spot now. it still runns 100 better then before i changed the midpipe and related, but something is definetely capping me on acceleration. i noticed them uffler looks dark in some spots, maybe from extreme heat from being clogged?
this is starting to get a little discouraging for me, and these miatas are starting to feel like trouble cars lol. its getting so bad, im thinking about just selling it

What year car?  If it's a 99 or 00 with california emissions, as most new england cars were, you may have a clogged pre-cat which is not unheard of.  A muffler getting clogged I think would be very unusual.

its a federal car, it definatelty feels clogged too

I recently removed my muffler to paint it. It had two hairballs (cat mesh material) in it. I could hear 'em rollin' around in there. I just shook it and turned it a few times, and out they came.