I have the E46 M3 vert and I like it a lot. The soft top feels totally insulated, and I have never felt like it is excessively noisy in the cabin. However, the convertible gives the M3 a slightly different feel. Its less of a focused sports car, but more of a cruiser, that still handles well and it pretty fast. I don't think I like a coupe more than a convertible or convertible more than a coupe. I just think they are different cars.
If I were you, I would test drive both on the same exact roads. Try to really drive them, so you can get a sense for how the convertible handles/ how straight line performance is affected.
Regarding mods, I can't help u much there, as its really not my specialty. Good luck with your decision, and post pics if you get one
Just wondering, are u going with 6MT or DCT?
afc1