OP, where in the North East are you? I'm about 40 minutes north of the old West Chester, PA Commodore facility, an A3000 fanatic, and a proficient electronics tech.
It's quite possible the Agnus, Amber, Paula, or Denise sockets are a bit corroded and could use replacement. I'd also swap the NiCad charge current resistor with a schottky diode, a new quartz trimmer, and install a low-profile 2032 coin-cell socket so you've got a proper working RTC. And since I'm a bit OCD, I use a GPS-disciplined oven controlled oscillator as a lab reference to calibrate the RTC.
Here's an example of a 3000 repair of mine, this was an eBay "for parts" motherboard I acquired this past fall. Cleaned, damaged solder mask patched up, new Agnus socket, CR2032 mod, and a new RTC trimmer...