It sounds like you might have the clutch pressure plate 'out of sync' with the outer clutch hub: they must drop together into their splines, but it is possible to assemble it with them standing on each other instead. It is easy to do this. It means you must go back in and remove the 4 little bolts again, EVENLY, because if this is the case, then the pressure plate is under great stress and can crack or break.
When you look at the clutch (with the engine's clutch cover removed) all the plates must be flush, flat against each other. This is the normal and correct appearance. If there is any space between them, the clutch was mis-assembled, and full-time Neutral is the result.
Also: the nut in the center of the clutch hub MUST go on with the curved side of the nut toward the curved washer, and that curved washer MUST be installed with the curved-out side toward you (hollow side toward the engine). If installed backward it can overload the threads on the mainshaft when tightening, and damage that shaft.
Another question: did someone else work on this engine before you got it? (And why did the clutch need to be changed? They last 80k+ miles or more.) Not having 4th or 5th gear is quite rare, and can result from having incorrect shim spacers on the far side of the mainshaft (from the clutch side), or from a damaged "R" shifter fork. If the cases were split and then mis-assembled it will have gears 1-N-2 and usually not 3 (and also no 4-5) when the "C" fork is not laid into the mainshaft's gear grooves at reassembly. Fixing this issue involves pulling the engine out to split the cases and put it back together correctly: I've seen these bikes for sale for $150 after someone did that to themselves and got mad, then just sold it(!).
