I cast my vote for muddling, Mitch, but my knowledge may be chock full of urban myth also. Replica builders seem to have different sources of donor Subaru engines: 1) they use a company that specializes either in running takeout engines or rebuilds with some kind of guarantee. Examples abound on the net, or 2) the builder shops for totaled Subarus with decent engines with fairly low miles, i.e., those with side or rear damage, no flood or fire, etc., then salvage engine, ecu, and any other bits and pieces they need: trannies, axles, suspension, etc.
The criteria of a decent price and not too high a mileage limits choices to models that have a few years on them. If they were newer, the engine and body would be worth enough to rebuild, unless damage was too extensive. Too old or too high a mileage, they go to the crusher.
The gremlins you reference above can and do appear, with poor connections and used wiring a frequent cause. Case in point: in one of my cross-country sojourns, I encountered an intermittent start fault, where the engine would turn one revolution, then quit. My shade tree skills were of no use.
I went to a "good ol' boys" Subi tuning shop in Flower Mound, TX, who were very hesitant to enter my briar patch, but were persuaded to try by a Texas-sized bucket of KFC original and 2 huge bottles of Mountain Dew.
Turns out it was a faulty key fob that was sensing a security issue and was shutting down the ignition circuit. I'd still be in Flower Mound if the diagnosis depended on me. The mechanic took out the fob battery and I was on the road again.
It does help to document all the data you can and keep it with the vehicle, i.e., fuse box locations, wiring color codes, ecu location and year, etc. The first thing the Flower Mound guy asked for was the wiring diagram. I gave him my best bland look and ran next door to the Colonel. YMMV.