Wish I would have seen this sooner. I could have saved you some hassle.
First, fix your clutch linkage. If the tranny doesn't want t go into gear you have a severe clutch disengagement issue. The mechanical side of it under the dash is the culprit. Possibly the hydraulic stuff, but it's not likely. Just because you think you see the pressure plate disengage (impossible in reality) doesn't mean it is fully. A 1/16" can make a world of difference on these trucks.
Second, the detent cups are not removed by drilling holes and pulling them out. This just drops shavings into the tranny and ruins the detent cups. All that's needed to get them out is first- note how deep they are installed and if they've been messed with by a moron rebuilder before. If they have, you could have some fun ahead of you. If the tranny has not been messed with take an 1/8" punch/drift and gently tap one side of the detent cup. Do this first thing, before you pull anything apart. The cup will easily rotate and when it gets 90 degrees from where it was the spring pressure will pop it right out and it will still look like new. If you pulled the case apart first then you'll need to stick a rod 1/2" diameter or so inside the shift rail bore to keep the detents up and put spring pressure on the cups.
In the case that a moron rebuilder has messed with your ZF and wallered out the detent holes, renstalled the plugs poorly or peened the hell out of the aluminum boss above the cups to hold them in I will do my best to clean them up, sometimes even going as far as welding up the holes and re-drilling them, but if the cups are just slightly loose what you can do is set the cup on a steel table concave side down and gently tap the top side with a hammer. You'll mushroom it out and can make it a perfect fit for the messed up hole this way.
To get the rear mainshaft bearing off the shaft I use a diff bearing puller that pulls it right off by the bearing cage. If you don't have one any shop that works on diffs should, it'll save you $40.
If the allen head bolts that hold the shift rail interlock plate on won't come right out don't strip them out. Just put some heat on the housing around and behind the area where the bolts go in. You can safely heat the case to 350 degrees. Those bolts will fall out at that temp.
Lastly, make sure you have the 1-3 thous bearing preload needed on the main and counter. I can't count how many shops think these things run bearing clearance instead of preload and build a ZF that comes apart the first time you put some power through it.