Any interest in contacting McIntosh or sending the piece to them for repair?
You could also measure every trace with your multimeter to check for zero ohms. There could always be a hairline crack in the trace. A lot of times, the trace will break close to the solder joint. Clamp test lead (if you have clips for your test leads) on the new caps wire leads and measure for zero ohms at the best place you could make contact, that will catch a hairline crack in the full run of that trace, if that may be a problem. There could possibly be a cold solder joint, and flux may be insulating a connection too. You can't just go by looks.
I've mentioned a couple of times in the past when someone ran into a similar problem, not to make a lot of changes at one time. I've had basic electronics ages ago, but never make that many changes at once. Those past threads seem to be gone. Even someone that does this for a living could run into this. So I just do new parts like that in sections, then test it. Then do another small section.
Also, when injecting a signal that way, use junk disposable speakers for testing. I must have picked up some RF while testing the way you mentioned 30-40 years ago. I wiped out a pair of tweeters that RF must have blown, I assume. Fortunately, they still had new replacement tweeters back then. After that, I always use junk speakers for testing first.
Another thing, especially replacing coupling caps, I'll try the new ones just one stage at a time. Then I bench test it, and if all is okay, then put the unit back in the system to see if I like the sound of the new caps. Plenty of times I didn't like the new caps. If I had done them all, that would have been a big disappointment for myself.
Hopefully you get it figured out. I thought I'd mention these things to save someone in the future from learning the hard way too. Maybe this will stay in the archives.
Old McIntosh units used rivets for grounding lugs, and willing to bet one or more of those has been compromised during the re-capping.
I have an old 'cattle prod' heavy duty soldering iron and acid flux from plumbing supply that I use to solder the ground lug rivets onto the frame they are attached to and this really helps the old Mac's. Never use acid flux on circuit boards, but it's perfect for soldering steel lugs to the steel framework.