Mine were 52 mm. You'll find that the right side pod fits REALLY snug against the frame... but it still fits. Ebay has a set of manometers to balance your carbs. Its really important to balance them after a rebuild. If they aren't the bike will run like a bag of crap.
As for the kick start. I believe the last year Honda had a 400 with a kick start was in 79..... and no... you unfortunately can not add one... (at least not with out spending some serious coin at a machine shop... and even then). I asked the same question about the bike after I did and engine swap.
The rebuild kit you but from Ebay doesn't have all of the parts needed for a complete rebuild. Some of the parts (like the little diaphragm on the Air Set Honda part number 16048-443-901 is stupid expensive (at least from the local guys). It basically a little leather and neoprene gasket the size of a quarter. I spent about 100 a piece and they supplied the lube (it was very gritty).