Well it's taken forever to find the time to post this update, but the big news it that I finally have my car running again!
Before installing the engine I had to reinstall the transmission and replace some of the shifting components... the throw out hub was very worn along with the shirt fork itself.

Two more videos from CM Autohaus that really helped make sure I did the install correctly can be found here:
https://www.youtube.com/watch?v=CRLIWmnToZAhttps://www.youtube.com/watch?v=wTduDCK6m_kI did run into a slight annoyance with installing the engine with a power steering rack. There is a bolt for the fluid line that collides with the rear cover plate on the engine. The trick to get over this is to tilt the rear of the engine up until the plate is just touching that bolt, then by hand just carefully lift the plate over the bolt towards the transmission. Then you can tilt the engine back in line with the bell housing and continue getting it aligned with the input shaft.

Another engine install tip... don't hook the engine up like it is below, where the chain does not have enough swing/slack. You need to be able to push the engine backward into the transmission. I had to pull the engine out and use more chain after I took this picture.
I originally hooked it up this way because I thought I didn't have enough clearance above for the engine crane.

After a lot of adjusting and shaking of the engine, it finally slid into the input shaft and the install was successful!

Fast forward another couple days and I have most of the accessories re-installed.

At this point I thought it was about time to start up the engine for the first time, but of course I hit another problem... leaks after filling up the coolant for the first time. There was a leak at the coolant hard line mating surface, and even a small drip from the weep hole of my new OEM water pump!


(the weep hole leak did stop after the engine started up, go figure...

)
I decided to fix the coolant line first, and just hope the weep hole drip fixed itself after start-up... the coolant line from Flo's wasn't exactly the same, but I made it work. I think the mating surface on the old line was too rough for the gasket to seal properly... but I kept it just in case I try using it again.

In hindsight, maybe it's worth filling the engine with water when it's on the stand, plugging the outlets, and test for leaks that way first? It was a pain having to take all the intake parts out twice.
After all this was replaced, and I refilled the coolant, I was ready to start the car up!
Very important tip here, I discovered my distributor was a single notch off and it was stopping my engine from starting up. Here is the comparison of where the rotor should and shouldn't be at cylinder #1 TDC.
Note that this is for my specific engine build, and yours might require different timing, but a single tooth off will stop your car from running.


Once I fixed my ignition timing, I let the car warm up, bled the coolant, confirmed no leaks, and started the engine break-in process.
I was having trouble keeping the car idling without stalling, so I had to open the idle screw on the throttle body all the way at first. I think there might not have been enough coolant in the IACV which was messing with the idle. Later I was able to tighten the screw back down and get it idling around ~900-1000 RPM. The idle is lumpy because of the Poncams I have installed, but otherwise it sounded great!

Here is a short clip of it idling, I've never had oil pressure so high at idle before...
https://www.youtube.com/watch?v=qny_Gk0XkvkFor break-in I was doing wide-open-throttle pulls from 2000-4000 RPM, and then 2000-5000 RPM in second or third gear, and letting the engine break with the throttle closed back down to 2000 RPM and repeating. I repeated this process for a few hours split over a couple days, I think about 30 miles or so of driving.
After that I changed the oil and filter, this was probably overkill and changing just the filter might have been fine, but I wanted to get as much metal from break-in out as possible.
The oil I'm using is Driven BR40.
Now the plan is to drive another 500 miles or so, and do one more oil change with non-break-in oil. I'm not sure whether to go with synthetic or conventional, does anyone have opinions on that?