I put a 1990 engine into a 2005 bike and then went to hook up the electrical connections.....
umm, WTF? Are any of the connectors compatible? Looks like a few hours of tracing electrical diagrams is in my future.
I believe you actually want to swap in several 2005 parts - neutral switch, signal generator, the plug for the hole where the older engine has a mechanical tach drive.
Is there a guide/thread anywhere on it?
http://gstwins.com/gsboard/index.php?topic=41261.0 (http://gstwins.com/gsboard/index.php?topic=41261.0)
That's got some of it. The neutral switch being different was mentioned in a gear indicator thread.