The -01 and -02 designators on the PCB assemblies are exactly what you have identified...revision numbers. What was revised and exactly how they are different you’ll never know unless you reverse engineer them, which wouldn’t be time well spent. Functionally they should operate the same, but I suspect part of what was captured in the revision was changes to the traces to eliminate the jumper wires. Jumper wires are fine and you’ll typically find those in PCB assemblies...quite common. Sometimes it’s a stranded and jacketed wire like that, other times it’s just a bare solid core “staple” jumper. Don’t sweat it.
Unless I’m misunderstanding what you are referring to with the cap with the sleeve, every aluminum electrolytic cap in your 388 has a plastic sleeve on it. You’re talking about the black plastic with the white printing on it? The cap body itself is literally a shiny metal aluminum can, the plastic is a shrink-wrap with the info printed on it which also insulates the can from possible short circuit.
Your high-pitched noise issue...really perplexing. I’m not clear...does the symptom occur even when literally nothing is connected to the 388? If so, tell me again in what outputs you can hear the noise? Go through EVERY output including insert send, buss outs, tape outs, AUX and EFF outs, monitor, stereo...everything. That’s my first step, where can I hear the problem, and under what conditions. Make notes. Then start doing stuff to see what you can do to change the sound whether it’s the nature of the sound or the level of the sound...what controls effect the sounds. Once you have that clearly identify you can start to isolate from what board the problem may originate, and then it’s time to get out the scope. A high-pitched sound like that may sometimes be an artifact of a much higher frequency noise you can’t hear stemming from an active component oscillating.