Hi,
A few dozen things come to mind on this: first start with the psu, check the 5v rail when your are loading it heavy,monitor it with a meter..it should maintain about 4.92v or better(some say 4.80's are ok,but my experience says otherwise). there are many many bad psu's out there,and 400W doesn't mean anything, its more important what the rails can handle individually.I've seen 400W pc power supplies that should be rated 250w..
Cheap/bad caps in the psu can also put out dirty power and cause lotsa troubles.Check the motherboard connector and the pigtail from the psu, notorious for having a bad 5v connection.checking power before the connector on the psu and somewhere near the power connector on the motherboard should show close voltage.
Assuming thats good, reseating chips-pushing on them is useless, pull them and reseat them(i doubt this is the trouble though) but we have 20 year old contacts here!Use a proper plcc puller, on those old sockets!. The pals and stuff on the side of the board you mention run quite hot normally,but usually run along happily that way.
I don't think heat is your problem but may aggravate the situation if you have a borederline component. Bad ram may very well be the trouble,and hot ram chips can be a sign of bad ram.This could cause most of the problems you mention and have effects system wide.
The wrong mask/max transfer values could also cause some of the troubles(may be a combination of things)But you said this combo ran ok before?.
Improper termination(check the diodes are the right way around,some 3000's had them soldered in wrong giving no term power to the scsi).Do you have the latest WD -08 scsi chip or the amd version?
Do you have a battery installed and looked at the battmem?Maybe a scsi setting is off there but this is doubtfull?
It could be your buster chip is flakey,you don't mention what revision??
Usually when you replace the PAL chips with GAL's they run alot cooler.Are you sure the replacements are GALS? Are the GAL replacements at least as fast or faster than the originals?maybe a bad replacement chip?
Capacitors could be going bad,especially after nearly 20 yrs, but i'm leaning toward bad ram,flakey psu or a flakey buster? Btw,what rev buster do you run?
This probabaly doesn't help much,being able to substitute parts with known good helps.
If you find the trouble,please report back on it.
Mike