The reverse rod was the issue in mine. On my model T18 (square top cover with 3 rails, 2 forks and a reverse lever inside the case above 1-2 sync) it is tricky to engage the reverse lever with it's rail.
In the end I had to guide the forks onto the 1-2 and 3-4 syncs, the get three corners worth of the cover fasteners installed, with shifter and trans in second gear, and then work the lever around a bit until the assembly fell into place.
I had the trans installed in the truck, and even ran the engine and engaged/disengaged clutch to help the process. somewhat messy.
I am posterity... Thanks for thinking of me!
I recently removed my T18 to replace the clutch and throw out bearing, installed it into the truck... thing is now i can not get the shifter stick in right. Is there a trick to it? It is in reverse gear.
First you need to determine if you have an earlier version or later.
Early version has 2 shift forks, and the reverse lever is bolted to the inside of the tranny. This lever fits into a shift rod in the shift housing that has a slot.
The 1-2 gears / sync assembly is towards the output shaft, 3-4 are towards the input shaft
Make sure the 3-4 assembly is in the middle, or neutral. put the shifter into second gear, and move the 1-2 synco assembly forward, so 2nd gear is in engaged.
After this, all you can do is jostle the assembly a bit, until it falls into place. start a couple bolts, use longer ones temporarily even, to help the process. make sure you dont leave longer bolts in place or try to tourque them down when your done.
I've only dealt with the earlier version of the tranny, dont know how difficult it might be with the later versions that have three forks on the shifter assembly.
The Ford Factory shop manuals, Volume 1 specifically, have the best diagrams and descriptions that I've seen.