everything sounded great until the upgrade

I own an old Marantz like that. It was my Dads but I am not sure the model at the moment. Anyway old Marantz is super warm and I used it on some bright B&Ws with good results. 
 

I am a musical fidelity fan and have heard them sound great on a pair of wilson Sophia 3… tons of bass slam. But in your situation I personally would sell it. While good no point in buying colored speakes to work around a sound you don’t like. 
 

Anyway nothing new is as warm as old Marantz really. I think some McIntosh amps are similar to Marantz’s house sound ( I own both McIntosh and Marantz). Maybe something like the MA352 would do the trick as it is a touch warm or older Mac amps. The newer ones from the current line are more neutral. 

Your new amplifier has revealed the flaws of your digital components. You need a parallel upgrade. Consider a better outboard DAC if you can use your current player as a stand-alone transport.

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..."

@grislybutter Under the hood, do you see those big donut torroidal transformers on each side?, and the two mosfet output transistors screwed into those heat sinks on each side... A nice dual mono class AB design. Letting those transformers bake and saturate a bit before playing will yield a different result too.

A quick and fun experiment to try one time. Leave your A3.2 integrated powered on for 24hrs straight and then listen again. Only need to try this once, 2-4 hours next time. Then, ratchet back from there until you find the warmup sweet spot for yours. My former dual mono SS torridal mosfet based amps sounded different at 1,2,4,24 hours. On critical listening days I’d let them warm-in for 2-4 hours, minimum of 2. Try it and see if you notice any difference or not. Should smooth out, sound a little softer and a little more musical too. An easy test if you wanna give it a go.

@decooney

Sounds like a harmless experiment, thanks! I will try it :)