I'm in the process of putting a new 235 into my '40 GMC. The trans and bellhousing were not painted at all. The original engine was blue/gray. But mine's a Canadian model and had a 224 in it rather than a 216 that it's US cousin uses. Your tranny paint should be fine. You can see photos of mine here:

http://community.webshots.com/user/ndnchf

Steve


See my 1940 Canadian GMC:
http://community.webshots.com/user/ndnchf