Hey Hanneman213, there's 2 bits to this (if I understand correctly):
Delay between patch changes - the last EPROM for MP2 is v1.41 (http://www.marshalljmpmodshop.net/miscellaneous_parts_and_replacement_tubes.htm). If your MP2 isn't v1.41 (displays when you turn it on) then this EPROM will make your patch changes faster (it was a problem in the early models (which I bought BTW)). But you also have to go into the System Edit menu, scroll (left arrow, 3 clicks) around until you find Program Change Speed, set it to Fast (default is Normal) BTW this is not available in the original EPROM, it was issued as a (very needed) update.
Now the pop/bump is another thing, I get it as well going from crunch/dist to clean, I get a pop if I'm still playing across the change (letting a chord ring etc). But my recollection is I didn't used to get it, it's come in over time (as I haven't changed anything in the patches). I get around it by making sure I make a space (in playing) while I change the patch, not ideal but works for now. I'm wondering if it's the compressor circuit/IC as I have that only on my clean patch but not on my rhythm/dirty patch(s).