edubs

I apologize for the extensive length of this, but this whole thing has been a long, drawn out process, and I’m about at my wit’s end! Any help would be much appreciated.
2000 Civic, 5-speed, 174,xxx miles
Mid March – Blew my engine, had it replaced with a junkyard engine (110,xxx miles) by a reputable, respected local mechanic. Also replaced timing belt & water pump. Picked up the car, drove it, heard some squealing & CEL came on out of town, once I hit 50-60 mph. Took it back & car wouldn’t reproduce squealing for mechanic. Said the CEL is result of o2 sensor (he had removed sensors from original engine to use on new one).
A week later drove 3 hrs out of town (mostly highway), left car w/ parents– all was well except for intermittent squealing here & there, not often. Parents drove my car while I was out of town, heard squealing, had brother-in-law mechanic check it – he thought maybe belt tensioner, wasn’t sure. On return trip to home, speedometer began bouncing around, then tach dropped, srs light came on, I pulled over & car died. Towed to a shop, they replaced my alternator (said it was completely seized up & this was probably my problem, not the tensioner), hit the highway and within 5 miles had a bouncing speedo again. Had system checked & Auto Zone, bad voltage regulator, took it back and they replaced the alternator again. Finished my trip – all fine except for cruise control didn’t work, but within 3 blocks of home the speedo was bouncing again and battery light flickered on. Took it to the mechanic who did my engine & he couldn’t get it to reproduce the issues. He did check the new alternator – good – replaced some ground wires & tightened loose heat shield, just in case those were the issues.
All has since been better, except for the occasional, intermittent squealing. The mechanic has heard it and tried to locate it, but it won’t continue long enough for him to trace it. Sometimes quiet, sometimes loud (seems to be louder/more often when cold outside), but occurs on cold start as well as after driving for some time. At its worse, seems to increase & decrease in volume & pitch with load. Two days ago, however, battery light flickered on when braking (Auto Zone charging system tested OK). Then today drove 30min highway commute to & from work for the first time in a while – car ran fine. Then headed out of town this evening and speedo started bouncing again and car idled really low & rough, as though it would stall, so I came home. Still squeals occasionally & CEL is still on. (Assumedly unrelated, I’ve also had brake pads & coil springs replaced.)
I carpool to work and have been avoiding driving out of town whenever possible due to these issues, so the problems seem frequent for as little as I’ve driven lately. I know little to nothing about mechanics, but this all seems too coincidental to not be related…What are we missing??