Hi everyone.
Thanks for the answers.
As for ticking floppy drive problem - I can't reproduce it now so I can't really say what the problem was, I suspect it has gone away after changing Agnus chip but I'm not 100% sure.
Unfortunately Amiga developed another floppy problem. Both floppy drives work fine for a 5-10 minutes then they usually they stop reading good floppies - WB shows bad sector while reading. After a power cycle they work again for next 5-10 minutes.
I bought new pair of CIA chips, I will try to replace them to see if something changes.
Like I said in the first post, I have changed whole PCB to brand new A2000 Remake so bad traces are really unlikely.
CPU is also "new" so eaten pins are not the case. Agnus also has a new socket.
As for yellow screen problem, today's troubleshooting session left me really puzzled.
At first I suspected SCSI HDD card because after returning to Amiga it suddenly stopped working and Amiga showed yellow screen every time it was in the system.
When there was only RAM card or bare system, everything worked "fine" (no yellow screen).
So I began to re-socket every chip on board because of infamous one-side pin contact sockets on PCB. After a few tries HDD card suddenly stared working after reseating SRAM chips.
On the other hand now RAM card is not working

Every time i put it in Amiga, it hangs on immediately and shows black screen, only sometimes it start booting but shows yellow screen again.
This has left me puzzled because RAM card was working without a problem earlier and "broke" because HDD card started working.

I suspect either Buster chip or bus drivers (less likely because they are brand new).
Other than that, Amiga is really unstable when it boots to Workbench, it sometimes hangs after several minutes. Also Amiga occasionally hangs when connecting keyboard while Amiga is running.