There are a handful of calibrations specifically listed for manual transmissions with these pcm's. There are no 305 or 350 manual trans cals. Here is the breakdown:

Code:
PCM               4.3                 7.4
6395            BJFD, BDXS         BHDB, BHDC, 
                BHDD

7427            BJWT, BJXJ,        BMHJ, BMHK, 
                BJWU               BMHL 

8625            BDXW, BBMW,   
                AYXY, BAAK, 
                BCPK, BCPL,
                BCPM, BDWZ, 
                BDXA, BDXC,
                BDZA, BDYX
This list was compiled using the following transmission RPOs:
mg5, mt8, mw1, mw3, and my2. No additional truck manual transmission rpos are known for the vehicles which use these pcm's. If you have a specific manual trans RPO you'd like to have checked I'll be glad to do it.