everything sounded great until the upgrade

I thought you bought it used so it might be the issue of broken in.  Here is a slightly negative review where you might find a tread of hint.  You might want to bypass the preamp section and try a good source feeding thru a good sounding DAC to MF.  Just a 2-cents.

https://hometheaterhifi.com/volume_10_2/musical-fidelity-a32-integrated-amplifier-6-2003.html  "... I compared the Musical Fidelity 3.2 to a PS Audio IV preamp and Bryston 4B power amp ... At the 60 dB setting, with the preamp in active mode, the Musical Fidelity A3.2 was a little less dynamic, and the bass response was not as tactile. At this level, the difference were very small, and almost indistinguishable, so if I were not in a critical listening and nit-picking mode, I would not have noticed a difference. At the 80 dB setting, the differences were a little more obvious, as the Bryston seemed a little faster on transients and the bass could be felt as well as heard. Whereas, with the Musical Fidelity A3.2, the bass was certainly heard but not felt to the same extent..."

Op, a decent DAC does not cost fortunate.  Quarter of the money you spent on the used MF could get you a pretty decent DAC that preserves soundstage width / depth, tonal balance, weighted bass well like Schiit Modius.  You could sell it on  eBay if you decide not to keep it to get good amount of money back.