The two issues that could be preventing it from seating: 1. it's cocked or crooked (not perfectly in line with the tranny output) or 2. it needs to rotate to index the splines.
By the way, Honda recommended (in a service bulletin to dealers) that the boot be sealed to the tubes. So, once you get your driveshaft reconnected, I'd use a little RTV (Honda recommends weather strip cement) on the surfaces where the boot seats. This will help to keep water out.
http://www.kb0nly.info/ATC/index.php...%2FATC250SX%2F
- Frank
1984 200ES Big Red
1985 350X (x2)
1986 350X
1986 250SX
1984 Auto-X
1984 ATC70
1985 ATC70