Just had my 5th gear go out, bent shift fork from what i know about these engines. seems easier more cost effecant to change out engine. i have factory honda repair manual but, it doesnt really give a step by step on removal / replacement. anyone else gone down this road before and have reccomondation of step by step manual i can use in conjunction with my factory manual. any idea what year engine is direct swap out for 06.
That's bad luck. You can use any GL1800 engine but the 01-05 have a different alternator and alternator drive gears. You will be able to use your 06 alternator in the older engine but it won't spin at the same rate because of the drive gear difference, and that means you won't get the same high output from your alternator.
I've had several engines out of GL1800's. As MichiganWing pointed out, if you have OE manual there is a step by step that'll point you in the right direction.
The only spec tools I can think of are the two sizes of spanner sockets for the locknuts on the left side frame mounts (they're adjustable). Also there's not enough room to get the engine out of the bike once it's loose...which is why front fender removal is recommended in the step by step. So a way to lift the frame/bike ass'y a bit is helpful. or you could remove the front wheel as well, which allows you to slide the engine forward far enough to come out. All this depends on how far your floorjack will allow you to drop the engine.
If you decided to repair your own (which is what I would do) you'd need a few more special tools. The only part of the repair I consider hard is assembling the cases. There's no room to get anything near the rings to compress them (and you're doing three at the same time). Honda's spec GL1800 plastic and velcro compressors are a huge help. You'll need a second person too.