Yes, it can be done I use later model parts all the time. Problem with 1995 and newer is the rough casting on the blocks and the shrouding really makes it hard to hide since you have to use a later shroud to clear ignition.
For an example this is a late 1970's small frame I redid for someone last year (this is a true mini bike spec engine in original tins) This tinwork ran from mid 70's-1984 so its correct for bikes that were still around at that point:
This was a 1995 small frame that originally had the fanblade style recoil shroud, but I used a 1985-1994 recoil on, you can see that they had to widen the shroud to clear the ignition change in 1984/1985. Still kinda gives that older look at least though, and with a few other older style parts, it does not come out too bad:
Alot of parts cross as well, as you can see from things that delray was saying. major changes to flywheel style limit to you the most because of its size and the taper they used. But the later they got the more universal they became, thats why alot of the OHV parts even cross with the L heads at that point.