All of us who wrench our own cars have been in this position so don't beat yourself up about it.
My worst was the Audi A4 1.8Turbo we bought for our 16yr old before we had the 318is drop in to our laps. It would start, run for about 5seconds and die... After reading one cause after another i ended up replacing the ECM, the fuel pump/filter, pulled and had the nozzles cleaned, bought two MAF's(one cheap jap and a brand new OEM$!), plugs, wires, coil packs, etc... All this and the car still didn't run longer than 5seconds.
It was the plenum that comes from inter-cooler to feed side of turbo... It had a nasty tear in bottom where you couldn't see and I picked that part up used for $28...

At 1st i was somewhat depressed and pissed at myself as I had leaned over and visually inspected the intake hosing but never physically removed to inspect and ended up with a few $'s spent that I didn't need to but what I gained from that(as you mentioned above) was a lot of experience/knowledge.
The car ran exceptionally after all the updates.