Hi, with regards to the 400s, the Barrel and pistons are (usually) the same on later twin shocks and early monoshock engines. I can give you the part numbers if you want but I dont think that you need them. The cylinder heads are the same for twin shocks and early monoshock engines (type 3VN1 and 3VN2). The later monoshock engines (3VN5) have a different cyinder head part number. I think this is normal for Yamaha to do this sort of mixing and matching, but at the end of the day MOST twin shock and monoshock engines have interchangeable parts (of the type you are speaking of). Hope I havent fogged the issue any more.
As for fitting the electric start engine into the kickstart frame....you will have to ask the question and I will try to answer it, there are so many detail differences, its impossible to let you know them all (that I found out anyway) in a post on here
Ian