I just bought an 2001 E46 M3 Convertible.
Was looking for the longest time. I was in the same boat as you. My search started in 2013 when I had my E92 M3 and then finally ended when I bought mine when I still had my 2015 F82 M4. Wanted a convertible for the nice weekends to pair with my E92 M3/F82 M4 and my E39 540i Sedan. Without a doubt look for a manual trans. The SMG is bound to fail and/or have other issues at some point. Be patient with your search and you'll come across one you'll like. No matter what, get a PPI done so they can check for subframe mount points and for VANOS issues. I bought mine from a private seller in Texas because I wanted to ensure there was no rust issues. Had the PPI done to make sure it had a clean bill of health before I wired the funds and had the car shipped back to me in NJ.
Click this thread here and read up:
http://www.m3forum.net/m3forum/showthread.php?t=189390
GL with your search!