I wouldn't get to worried about the little things. The GI Joe Harley WLA 45 is slightly off dimensionally (about 2" too low and 8" to 10" short in 1/6th scale) and is missing a couple of items that would stop it from actually running if it were a real motorcycle. Also missing the toolbox and some other detail items. But overall not a bad representation of a classic "Liberator". But the real reason you shouldn't get too tense about the little things is Cap's bike in the movie isn't an original WLA 45. It's a custom HD put together with Joe Johnston and the Marvel Studio's guys to evoke a WWII look and feel. The GI Joe bike being a little small is the least of your problems if your going to start counting bolts. No WLA is even close to Cap's bike in appearance. Still think it will make a great display piece to go with Captain America and you should enjoy it for what it is.
The New Ray Indian does not in any way represent any actual US WWII Military motorcycle. Much more of a toy even than the Joe bike. Still fun, but not accurate to any real subject. Some of the civilian bikes look great to me though. To each his own.