Almost everything internal will swap.
Exceptions:
1. Pump, or rather pump shaft. 2008+ has a longer shaft I believe
2. Midshaft housing. 1990-1993 use a smaller housing that will bolt up to later hulls. If you have a 1994 or 1995 SN hull, those housing will work fine in all later hulls.
3. Steering cables are not interchangeable between 2008+ and previous year SJ's, unless you also replace the stock 2008+ pole.
4. ?