Hey everyone, thank you all for the great responses. I'm going to try and answer some of the questions posed and give more information that was requested.
One important note. I just discovered that there are several different revisions of power supply boards. This could account for the very different sound between units. I tried swapping one board from one amp to another ( thinking... ASSUMING they were all the same ) and it didn't go well. There was an electrical "buzzing" sound from the amp, and the heat sinks got rather warm from being on for 15 seconds. ( these amps run at room temp unless you are really driving them hard ). So apparently im not 100% sure the schematic I posted is for this particular amp revision.
I do have the service manual that I have attached below. I purposely didn't list the name of the amp because most people see the manufacture and dismiss it as junk. This particular amp was designed by a different company and then rebadged by Alesis when it bought out the company in the 90's. It was made specifically for the monitor Two speakers ( not the monitor one MK2, The monitor Two, a three way speaker - Pic below. ). It is for a Alesis RA500.
The part I am trying to replace actually blew during a very heavy bass passage. ( pic below ) It also took out the woofer on that side ( voice coil came loose and is now rubbing against the magnet structure. ). I have 4 of these amps, and only one sounds what I would describe as "transparent". All the others have a differing "Tonality" to them. As for the comment that it was "different speakers", I replaced the blown woofer with a spare before I discovered the amp had a problem. It sounded the same as it did before. I have been doing sound for almost 40 years ( studio, live and recording ) so I have a very good ear for hearing subtle changes. But honestly, anyone that would A/B these would easily notice the difference. With the replacement amp, the midrange went from "existing, open and revealing" to "harsh, screechy and bright". Not a subtle difference at all. The Bass now is very "Boxy" sounding, not going much below 80hz. All sources, A/D converters and such are exactly the same. The amp is the only difference. So I get the skepticism, but trust me when I say it's the replacement amp that is making the difference. I do plan on pulling the "bad sounding one" apart after the main amp is back up and seeing if someone changed the output transistors with "Bob's Brand" parts. I can still get the original transistors, so I am planning on rebuilding the second amp when I can. Anyway, I'm guessing that is where the difference is. Honestly, the listening experience went from "Holy crap, I can hear something ive never heard in that classic recording before" to more of a "Big annoying cheap boom box" type of sound, just from switching the amps.
Anywho, I got on a bit of a tangent there. I thought at first the big caps had started leaking and that shorted the part out ( you can see something on the board in the photo ). Turns out one of the neighborhood stray cats had snuck in the studio and marked the rack above the amp, and that had dripped down on the board and apparently shorted it out during loud passages. Initially, ( before I knew about the cat ) I was thinking it was a cap leaking. I removed the caps planning on replacing them and realized there was no electrolytic under them. The white glue had sealed the underside, and there was no "pee" under them. Using a powerful infrared light source the "Goo" floresed brightly. Luckily all the traces are on the backside, so no corrosion damage. The caps tested well within spec, so those are going back in.
I do need to replace both smaller caps so they match, but after reading some of the responses i'm thinking I may have been over concerned about how this may affect the sound. On high end amps, it's common practice to put a smaller cap across the main filter caps to increase high frequency capability ( Ive heard this from multiple high end amp designers on several podcasts ). Im guessing it may have some truth to it? Being the amp tops out at 70,000 HZ ( my cat can attest that it goes higher that 20K ) I'm leaning toward the possibility that this cap matters. It may not, but I don't want to loose the way the highs sounded before.
Side note, I get that I may be overthinking this or coming off as an audio snob, ( im definitely not, I have Alesis equipment ) but every single person that listens to these speakers on that amp spends at least 15 minutes pulling up classic recordings, then sits there with their mouths open and eyes wide. They always make the following two comments " I've never heard that before" and "The hairs on my neck and arms are standing up". These aren't the best speakers ever made, heck, I have 4 pairs of them and only one pair sound even remotely good ( I got all them used ). But for what they are, they are remarkable, and I don't have 4 grand to replace them with something comparable. Hence, why I am so passionate to repair the amp to its original performance. Thats why I am asking the professional community what you all think. It's very possible I am completely missing something, or overcomplicating a simple solution.
Thanks everyone.