Did you change the pilot bearing as well or leave the old one in there?

 

put the trans in gear and spin the output shaft to align the splines of the input shaft.

 

X2 and realize that getting the transmission seated is often a matter of only a slight 1/8" up or down movement of the transmission jack to get the transmission at the correct angle so it will suddenly slide into place.

Whatever you do don't try to pull the transmission into place with the transmission mounting bolts as that can break or strip the threads!

 

Having done this recently and having the same problem, here are a few things that might help.

A clutch alignment tool will help you since you can match the splines directions on the clutch and the transmission shaft to make it as close as possible, that way any misalignment will work it self out.

One of the few times I would disagree with Jerry.

Once you get the shaft into the clutch and the transmission as close as you can, use the bell housing bolts to slowly draw the transmission and the engine together, I think I was able to get three of threaded, on one each side and one near the top. Do this carefully and slowly, a few turns each time, alternating bolts, moving the transmission evenly until you get it mated up. You want it to be slow, so you don't crack the bell housing. That was what worked for me after probably an hour trying to muscle it back together, a mechanic friend suggested I do it that way.

 

Once you get the shaft into the clutch and the transmission as close as you can, use the bell housing bolts to slowly draw the transmission and the engine together.

That sounds like a good way to damage something that isn't lined up right.
If you can get 2 bolts started, do so but only a few threads, then jiggle/shake/wiggle the trans until it drops into place

 

With as much separation as you are showing, I believe your input shaft splines are not lining up on your clutch splines. Provided of course that you used a clutch alignment tool and properly centered your clutch, all you may need to do is turn your output shaft in tiny increments while offering the transmission up and they should align and allow you to stab it forward. From your photo, it is hard to tell, but the angle of the engine must match the angle of the transmission in both the up-down, and side-to-side perspectives. It doesn't take much at all to misalign, and things won't slide together.

I seriously avoid using the mounting bolts to draw the bell housing/tranny up to the engine. Sorry this task is so frustrating, but I'm sure if you keep fiddling with it you'll get it together, sounds like you have the right tools.

 

Did you check to be sure that the splines on the disc match the splines on the input shaft?

 

I am also in the camp of do not try to pull the transmission tight using bolts. I have seen a number of bellhousings that have been cracked or had the mounting ears broken off because of this. One way to help with the alignment is to take longer bolts and cut the heads off, then thread a them into the block and use them to align the bellhousing to the block to assist with sliding everything together. Also previously mentioned, make sure the clutch is centered up using the alignment tool.

 

Functioning example of alignment dowels as described. Blue tape there so you can see them better in the photo. I don't use all-thread as it seems to act like a file on the alum bell housing bolt holes and also tends to hang up.



These help align, and also take the weight of the front of the transmission so you can wiggle the back end around, raise, lower etc to get the perfect alignment to stab the thing home. Don't make them more than about 5-5 1/2" long or you end up with interference between the bell housing and the sheetmetal of the firewall/transmission tunnel.

 

Thanks everyone who responded!

I was finally able to get it into place using the long bolt trick, as well as putting it in 3rd gear (moved shifter forward and easier to angle into the boot area) and turning the output shaft on the transmission.

Once I did the above tricks it slipped into place nicely up to the alignment dowels, and they would rest in the slots but not go in fully. So I carefully used the bolts, a few turns at a time, to tighten it down the last 1/4 or 1/8 of an inch. I made sure to go slowly so it wouldn't crack, per advice everyone posted.

Now the jeep is throwing a ton of other problems at me, so I get to cross that one off the list, and add two more! I appreciate the input everyone.

 

Oh, forgot to mention, the reason they wouldn't go in the last tiny little bit was because the o2 sensor loom got pinched at the very top. So I had to loosen all the bolts I tightened on the bottom and pry it back off a tiny bit, then pull the wires out. It slipped almost completely in place that time and I was able to easily snug it from there.

This jeep I swear. It's like giving a cat a bath

 

Yep watched a friend crack a bell housing once using the bolts to snug it together.... Oops.

 

Anyone ever encounter rusty dowel pins? Drawing a bellhousing to the engine with bolts is common practice at shops and dealerships everywhere. While I agree with Blaine that if the trans doesn't drop in place easily that you should stop and find out why. But when you find no other reason than dowel pins that are sticking then using the bolts to pull the tranny up to the engine is absolutely acceptable.

And don't be nice to the tranny while trying to mate it to the engine. Grab that thing like it just slapped your sister and jiggle and shake and wiggle it until it slides on. You won't hurt anything.

 

But when you find no other reason than dowel pins that are sticking then using the bolts to pull the tranny up to the engine is absolutely acceptable.

The problem is that just because someone can find "no other reason" the transmission won't seat, that doesn't mean there isn't still a very good reason... like it simply still isn't aligned properly which is the most common cause.

Every time I could find no other reason for a transmission to not fully seat, it always ended finally seating into place once I got the angle right. Using the bolts to pull a transmission in that isn't aligned well enough to seat is just asking to break something major. You can't use the bolts to pull a misaligned transmission into place and a small misalignment bad enough to prevent it from seating often won't be visible.

 

a small misalignment bad enough to prevent it from seating often won't be visible.

I think that's the major problem here. NOTHING is visible during this procedure!!

 

Yep, thats why you have to be aware of all the wiring up there. I just replace my motor a couple of weeks ago. I can't tell you how many time i checked the wiring wasnt getting pinched.

 

Well, when you consider that the purpose of a 2-ton engine hoist is to determine the tensile strength of all the things you forgot to disconnect prior to pulling the engine..........