I'm running into the exact same issue as the OP. 1/4" gap all around. Used the bolts to pull the transmission towards the engine and get it lined up. Both dowels look to be in the transmission casing. But then when I screw in any of the bolts further, there's suddenly resistance. Didn't want to apply too much pressure and mess up the clutch disk as I was afraid the input shaft splines weren't lining up with the disk. But from what I've read, it looks like it's more than likely lined up, at least I'm hoping. I'm going to try what you guys did to see if I can get the transmission on all the way. I saw I might have had to put it in gear, but it didn't seen feasible since my slave cylinder is off and the gearbox isn't connected yet since the back end of the transmission is still disconnected.

 

You don't need the clutch working to shift the trans while car is not running. So not a problem that slave is disconnected.

The idea is once in gear, you can rotate the splned shaft so it aligns with clutch disk by rotating the trans output, the prop shaft mount plate. You want a higher gear for this. So if spline alignment is the issue, rotating shaft with trans in gear is the solution.

You can also remove the fork from its holder (but still inside trans bell housing), and pop into place after trans fully in place. That way you know its not what is holding things up.

 

Tried to use the pry bar on the fork today. Think I used a decent amount of pressure. Didn't budge. Decided to try and put the shifter in gear. Seems it won't engage in any gear. That doesn't seem right at all. So I went ahead and started unbolting the transmission bolts. Figure I'll try to put it in gear after that and see how that goes. Slightly stripped the threading on one of the bottom bolts... This is such a headache.

 

You cant pop the fork if its jammed in place. Gotta back trans off a bit, then pop fork outta its holder, then trans to block, then pop fork back into place.

Or, as you slide trans into place, one hand on fork, articulating it into place as trans slides forward.

 

The fork isn't blocking the transmission from going into place. Took off the bolts and backed it out. Splines look fine. I might try unbolting the bolts from the pressure plate slightly and slide the friction disk onto the input shaft spline so they're lined up. Then torque it slightly. Then slide the transmission back into place and try to torque it to specify through the hole for the fork. Someone mentioned they managed to use that unorthodox method to get it to work. Cause I have no other idea since I can't get my shifter into gear for some reason. I unbolted the 4 bolts from the inside of the car that were holding the shifter to the top of the back end of the transmission as per the DIY guide. I wonder if something got caught up. I didn't remove the shifter itself.

 

Make sure the fork isnt pushed into place before sliding the transmission back on or else itll get jammed. Use a shop towel or something to keep the fork from falling into the transmission housing then wiggle it on back and forth. Once the tranny is on completely, carefully push the fork back in to engage it (dont drop the fork or towel into the case or else youll have to take the transmission off again).

 

Once again, fork isn't an issue. I'm starting to think maybe I should detach the drive shaft so I have more room to work with. I took out the back of the transmission with just enough of a gap to remove and replace the parts. But now when I try to put it back in, the engine is slightly slanted down and the transmission and also slanted, but in the opposite direction. Like this / \. So the back end is sometimes getting caught on the top of the drive shaft. I think that's causing the tip of the input shaft to be too off and get into the pilot bearing. I mean the drive shaft should be pretty quick to detach and reattach right? That should allow me to lower the back end of the transmission enough so it's on the same slope as the engine and get the input shaft lined up with the pilot bearing. For reference the top of the transmission is about 1/4" gap and the bottom is about 1/2" gap right now.

 

The propshaft to diff bolts are just as easy (or not) as the shaft to trans bolts. But maybe all you need to do is remove the safety strap and let shaft droop out of the way.

 

The fork is not blocking you. The reason for activating the fork is to disengage the pressure plate. This lets the disc center itself, as the pilot bearing may be blocking the transmission.

But yes the trans and engine need to be dead straight with each other. Equal finger gaps top bottom left and right.