Well personally i run:
1x Sonarman
1x Planesman
2x Torp (You'll only need one for front T slot in SS4/SS5)
3x Engineers* (You dont need this many 2 works)
1x Repair (Extra)

*Engineers are a must because IJN subs are REALLY slow.

Torps do cap out but as for when im not sure, still try to get some +11s

Planesman as far as i know doesn't cap, but Sonar does.

dont bother with repairers, engies all the way

You will want a minimum of four engies for the SS5.  Try to keep them all at the same level for best results.  I ran two sets of crews until the subs could fit them all in it.

The torpedo men do seem to cap out.  I don't know for certain how high it is, but somewhere around level 80 it no longer seemed to make a difference what skill level they were at.