The culprit of my woes, a broken weld on the shifter shaft inside the case. It is the very first part to go in the transmission so it required complete disassembly for replacement.
I'm pretty sure I broke the old part from abuse. My clutch was acting up for quite a while due to a buffer steel plate that the rivets fell apart. The bike was hard to shift due to poor clutch action and I was really hard on the shift lever. I'm sure the added stress from that caused the weld to break. The moral is fix your clutch when it acts up and you won't have this problem.
The new part is made by Baker. It has an improved pawl spring so that won't break on me in the future.
The gear set was in good condition and should last a long time. I've spent alot of miles on many different Harley's with the 6 speed transmission. I like the 5 speeds better. They are stronger.
I've owned this bike since May of 2010. It had 54k miles on it. Currently it has 93k miles on it. I put a new cam and tappets in it @ 67k, upgraded the stereo and speakers @80k. I've had just about everything on this bike apart besides the short block. It's going to require a major overhaul eventually but for now it's running good so I'm just gonna keep riding it. The long term plan, at about 120k or 2 more years worth of riding, is an S&S stroker kit, another new cam, and new belt and sprockets. An 89 c.i. Evo is sure a fun motor in a touring bike.