We have a 1981 RX-7 with the original motor taken out and we're installing a 1982 12A into it. Got the beehive oil cooler off and the original oil cooler back on. Have the clutch aligned, but for some reason, the motor won't go the last inch or so onto the spline of the transmission.

We can see where the grease on the spline is pushed back so we know that we are aligned and on it OK, so is there something obvious we're missing or do we just need to jiggle it for another 3 hours, or wiggle the shifter?

 

Sounds like the starter is stopping things. Is the starter needs to be out.

You're going to feel great when you get the engine in, and everything is sorted out.

 

Yup, the starter is out.

 

Pull the engine back out and clean out all the grease you have packed into pilot bearing
Inspect end of input shaft on trans,look ok?
is the pilot bearing new? Put your little finger inside bearing and turn,is it smooth? Look closely at it,are all roller bearings there? Do you have a grease seal on top of pilot bearing? Are they both seated to proper depth in e shaft?
If yes to all questions, smear a small amount of grease on little finger and work it into all the rollers of pilot bearing,just enough that you can see the presence of grease on rollers but can still see them.
Wipe whatever’s left on your finger onto input shaft of trans. This is a situation where more grease is not better. Too much grease in pilot bearing,with seal in place,will not let input shaft of trans enter bearing-no matter what you do-it’s hydraulically locked out.

Hope the trans has not been hanging that amount of distance all this time,that alone can cause problems.
I know,one more time...put your clutch alignment tool in place before you clean grease out and after to be absolutely sure it can go fully into pilot bearing.

Put clutch alignment tool in and if correct tool slides in with ease,the trans will slide in same way.
My money’s on too much grease in pilot bearing.
Post back results,success or....

 

Had this exact issue just a couple weeks ago, and I've got to say, avoid the desire to just crank the engine and trans together with bolts (I am unfortunately speaking from experience). After fighting with it for a half hour I finally gave in and mangled the bearing something awful, or at least it sure sounded terrible with the clutch in. I've got a new one so now I'm just waiting for the time to do it, but anyway, that's that not important. GSLSEforme's advice about too much grease is my bet too. Either that or perhaps you were shipped the wrong bearing which is supposedly somewhat common, although I haven't run into it across my short experience with rotary's.

 

I always test fit the Pilot Bearing onto the I put shaft along with the Grease Seal maybe because I'm visually mechanical about some things, but it does prevent installation of the wrong parts.

As usual, GSLSEforme has this one nailed, and removal of most of the Grease on the Pilot Bearing rollers will work. Even then, it's a case of slowly working the trans onto the engine while allowing air to exit the Pilot Bearing space. Sometimes it takes awhile,... move the Trans Jack forward, go get a drink of water, move the Jack forward, go to the bathroom,... You'll get it seated.

Avoid the tendency to grab channel locks and start squishing down mounting bosses - that's a good way to crack one off. A member here used some all-thread of the right diameter and pitch to make guide pins which he then used nuts to tighten the trans to engine - smart idea if you're impatient, or do this job frequently because you slip clutches!