Well, I'm not completely clued in the progression/history of your project, but the impression I've gotten is that you've been a bit of a slave to other people's schedules in waiting for stuff to get done.
I think my main question here is in relation to your 'stage 1 engine install' taking four years. How much of that time was spent waiting for other people? If you knew then what you know now, would you be satisfied with such a long time span? Would that perhaps have motivated you differently in choosing to perhaps learn the necessary skills and doing it yourself rather than farming something out?
That's a reasonable question. I would say that yes, a big part of the four years was spent waiting other people. Everything about this installation is custom. The only place that the engine has an interface with the rest of the car that follows the factory form is one of the engine mounts. Every other linkage, bracket, hose, pipe, mount, and wire is custom. I designed all of these interfaces and fabricated them, farming out only the welding, which I don't do.
I ordered the long-block, header, and intake (minus air box) from UNITEK. The engine was great (so far), except for the cam-carrier being poorly sealed to the head with RTV. The header was not properly designed to fit in a 240, requiring modifications to both the header and firewall. (The struggle with the airbox and hood has already been discussed elsewhere.)
Before this install, the most complex thing I had ever done was a transmission swap. Everything I did was trial and error, mock-up and test fit, etc. Everything I did was the first time I had ever done it and I had a LOT of do-overs. When you are asking other people for work that is one-off, that they've never done before, and you're not willing to pay for their full-time focus, your work gets attention whenever they have spare time from the stuff that really pays their bills.
On the stuff I designed and made myself, I got stumped a lot. I had to take breaks and do research, order parts and fittings, wait for them to come, realize they wouldn't work, and then do more rethinking. I had, on average, less than 10 hours a week to dedicate to this project, including weekends. There were many weeks that I never touched the car.
Just this last tuning session took 3 months. My dyno operator is exceptionally well qualified but had never seen an Omex EMS before. The details are not like MOTEC and the other systems he designs and installs. He spent a lot of time on my car that he did not charge me for. As a result, I was not his first priority.
Would I do it differently if I had to do it over? I don't think so. The other priorities in my life are much more important than this project. Learning to weld would have been the only other skill I could have learned that would have helped, but the time I would have spent learning to do the quality of welding I paid to have done would likely have used up the time it saved. (But I still wish I knew how to weld.)
Were I to start this project today, I would obviously chose to work with Knox or RSI or JVAB, etc. to have the engine built, but when I ordered it 6 years ago no one in the US was building full-house turbo redblocks to spec.