Don't think its necessary to revert to an older MB just for the clock.
Key point is: If your machine is keeping time fine when it is running then there is nothing wrong with the RTC. It is most likely that the RTC chip isn't happy with 3v battery of the replacement 2032 kit. If you have an old portable phone battery 3.6v you might try that. My old A2000 was fine with a 3v coin battery but my new one isn't. The RTC needs 3.6 v. 3v only is sometimes not enough in my experience.
You've done heaps of good work don't throw it away. Try one of these first:http://www.ebay.com.au/itm/NEW-LIR2032-LITHIUM-ION-3-6V-RECHARGEABLE-COIN-CELL-BIOS-BACKUP-CMOS-BATTERY-/140705458330?pt=LH_DefaultDomain_0&hash=item20c2b2e89a. If that doesn't work check the continuity of the tracks from the RTC chip to the battery.
Hi i Had the same Problem with the coin battery from amigakit with my A2000 it turn out that if heated to long when soldering the track at the back of the coin cell on the board looses contact which might have happened to you as well,i had to by a new one and use a very short solder time to make sure i didn,t damage the back of the coin battery board, which i think is what happened in you case i hope, check the tracks from the soldering points for the battery on the motherboard to the rtc clock if they have no breaks then its the coin battery that is defect. GOOD LUCK.
