Are there any issues when swapping a late model ('03) engine and transmission into an older ('86) savage?

The engine has a few electrical hook ups.
Generator/regulator, common connector, but check number of wires.  Most are 5 wire, but heard there are some 3 wire.
ignition sensor, common connector.
neutral switch, common connector.
sparky, common connector.

Not engine related, the kickstand sensor has a different connector on the '86 thru '88 than later years.  And the front brake light has a different switch on the early years.

Something to be aware of between '86/'88 and later models.
The CDI has different timing.  Not sure which years are different.
Safest to get the CDI for that year engine.  But any '95 or later CDI should work with any '95 or later.  And any '86 thru '88 should work on those years.  Not guaranteed though.