Interlaced video: the video syncs are generated by Agnus - so possibly it's bad. You've ruled out the monitor I guess? When using the flicker fixer, do you mean the 31 kHz signal also gets jumpy?? Very strange...
RAM: the sizing works through pin 12 only. On the 3000, there's J853 required at 1-2 (2-3 for early Ramseys) but it's not present (hardwired) on the 4000 afaik. What happens if you set the jumper to 256Kx4?
I'd trace/measure the CAS and RAS lines and all address lines from Ramsey to the first slot to make sure they work (if they didn't the machine shouldn't run but the problem must be somewhere). There are no sense lines from the RAM slots, you can rule that out. Other than a bad line (contact? solderpoint?) pretty much all there's left is Ramsey itself.
Pretty weird things can happen when decoupling stops working (capacitors) but once they're very bad everything'll get pretty unstable.
