You ask a lot of questions, methinks! I can't answer them all but wonder if you created the partitions using PartitionMagic? If so, you can get all the answers from their program resource material, I would think, and it will be accurate and appropriate. If you partitioned manually, then answers as follows:-
1.No, the D partition could be FAT 16 if you want, but it may depend upon what you use it for.
2.Can't comment on the swop file location.
3.I don't think you can delete My Docs from C, but you can redirect the Desktop shortcut by right-clicking and selecting Properties, then amending the command line to point to the new location. It may offer to move all exisiting files from the old location to the new for you too!
4.I don't know the appropriate size for the C partition but it will vary anyway depending upon which OS you're using. The question suggests to me that you're going to instal progs and applications to D? Be aware, just a few programs will only run properly from the C drive.
5.You haven't given enough info to make comments on the snags ot otherwise of that arrangement. What OS; what working arrangements; for what purpose; etc?