I started off by removing the bolt that holds the coupler and putting a drop of loctite to make sure it doesn't come out. Even if it did the coupler had to be pressed on and I can't imagine it will ever move again, at least not without using a puller.
Then I attached the spacers and adapter plate to the motor. Again using some loctite and torqued these bolts to 40 ft lbs. With these bolts, and despite them being recessed were still very close the flywheel so I shortened the heads by .07" each using a bench grinder. I didn't want to risk them rubbing after perhaps the motor and transmission warmed up.
Next the flywheel was bolted on. The original specs called for 90 ft lbs of torque but I dropped this down to 70 with a small drop of loctite. The original crankshaft this was on was a hardened steel. The steel we are using is considered soft and I didn't want to risk pushing the material too hard and strip out a hole on something that took so long to make.
We can now attach the clutch and clutch housing. This part can be tricky if you've never changed out a clutch. You'd think they'd design these different to avoid the problem but they don't. The problem is the clutch itself needs to be centered with the housing, and therefore the transmission input shaft. If you simply tighten all the bolts the clutch will probably be too low (gravity) and you'll never be able to push the transmission and motor together. Usually you can just buy an alignment tool that you slide in while you torque the bolts. I didn't have one so made one out of a 17mm socket and some electric tape. It wasn't perfect but allowed me to slightly move the socket on an extension until I could see it was aligned before tightening the bolts. These bolts called for 19 ft lbs and again I used just a small drop of loctite.
Next came the hard part. The two guide pin holes we drilled are very slightly off and it requires some elbow grease to get them started each time. After I finally got it together I realized the clutch arm had fallen out and I had to start over. This is a reverse clutch and it actually pulls on the clutch instead of pushing into it to release. It makes hooking the clutch arm into place tricky and has to be done at just the right time while you're mating the motor and transmission.
Now the grand finale! I was so nervous to apply the 12v to the motor afraid I'd hear some rubbing, clanking, or just see the whole unit vibrating badly. All of this of course unfounded since I witnessed all the machining work. So I wired everything up and then touch the final wire to the battery. Luckily the transmission cross brace was still attached because that's what kept the whole unit from falling over as the initial torque kicked in. The motor always instantly reached its top speed for 12v and output shaft of the transmission was spinning happily along. Very quiet, very smooth...woohoo it works!
Of course the initial test wasn't enough as I was just too excited. I had to go get my wife, bang on my neighbors doors (he helped me strip the car down originally), call my uncle, try out a few of the gears just to see the output shaft spin at different speeds.
Here is a quick shot of the completed assembly after the 12v test.
Another shot so you can see another angle.
Next comes hoisting the motor/transmission into place in the car and taking measurements for the motor mount that needs to be built next.