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Well I finally figured out my problem. I had to grind the shift fork down some. I found a couple other posts where people bought the shift forks and said they had to grind them down.
M5R2 shift fork grinding down
After I ground down the shift fork I could use my hands to manually more the forks to the neutral position or to one of the other gears. After getting it back together it dropped right onto the transmission.
Here is what I did
Take the top cover off
Take the top cover plugs out
Use a flat punch to drive out the spring pin. Check your clearance to the top cover while driving it out. Drive out the other spring pin on the other rail.
Turn the top cover up on its end and slowly start driving out the rail. It should go pretty easily. You don't need to drive the rail all the way out. You need a long punch or I used a long bolt along with the punch. When driving out the rail be careful not to lose the ball bearing and spring.
When you drive one of the rail down watch for the detent pin to come into view and just tip it on it's side and it'll slide out. For the ball bearing I just left my punch in and as you push it past the area it will hang up on the punch. Then slowly remove your punch and you should be fine.
Slip the shift forks off and go in reverse order.
When you get them installed check to make sure that you can move them back and forth a little. If not check if the shift forks are rubbing up against each other. I took a small piece of paper and checked the gap. After marking and removing I took it to the bench grinder and just did some slow passes to try to evenly round it out.
When I replaced my rubber end plugs I found part# 555-108 at Oreilly's. And I had to order a missing soft plug for the other end, part # 219-1135, which I found at Rockauto.
To reinstall I made sure the shift rails are in neutral. You can tell by looking down the top and all three will be lined up across. Actually I don't think it matter what gear you're in as long as the transmission and the top cover rails are in the same gear. Once you have the top cover in the truck just tip it over the transmission and make sure the shift forks and the synchronizers line up. If they don't just move them by hand to line them up. The top cover should slip down over the synchros without much fuss.
Anyway, hope this might help the next person who replaces their shift forks.
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