The trace wires you are observing... are they just toward the rear of the daughterboard? If so, there are 4 PAL chips that many people have wired between each other. The grounds that is. FWIW, I have owned about a dozen A1000's since 1986 with various internal and external expansion devices and not once have I ever needed to perform this supposedly necessary grounding mod. Same with the expansion bus power supply ground mod. BUT... maybe users of the sidecar or some other peripherals "needed" the extra help at some time.
RE: those 252180 & 252179 chips, your computer wouldn't boot at all or show the Kickstart icon upon startup if they were bad. I'd leave 'em alone or maybe re-seat them is all (same with all socketed chips, especially the CPU. Re: the faux Kickstart chips under the disk drive, I've got both CBM and what looks to burned, as you've got sitting there. Same revisions and part numbers.
The ceramic/gold/mil spec chips were in the original A1000's. Look for the revision number at the end of the chip numbers. You'll see R4, R8, etc. Later revision will be the plastic ones as you've noticed. You might even have the Denise that allows for EHB modes if it's late enough :-) Originals did not do Extra Half-Brite.
Oh - and are your drive ribbon cables okay? If those go bad, were crimped because of peripherals, female connectors no longer tight, etc., they can cause a drive to act flakey. This just happened to me involving an A2000 drive I thought was bad. Turned out the fault was with the cable!