Just got my first A2000! :)

[gertsy]

Congrats.  Rev6, 040 Accelerator and 16bit sound card. Good get!
Hope you have lots of fun putting it back together.  Any mild cleaner and old tooth brush will remove the alkaline that's leaked from the NiCad. Don't use vinegar cos it stinks. Warm water with a mild detergent will do.  If there's any remaining corrosion WD40 or RP7 on a cotton bud (q-tip?) should clear it. You might need a scraper/pin/jewellers screwdriver to carefully scratch any corrosion from metal parts. Don't scrape the mboard or tracks unless you know what your doing.
You might want to check the connections on the front right of the 68000 pins and socket, as they are fairly close to the battery and can sometimes get corroded
Make sure everything is wiped and fully dry before reassembling.
You can use a hair dryer on cold or warm (not hot) and low speed. Keep it a fair way back to reduce the possibility of static build up.

I remember doing this. Ahh it's fun bringing the old girls back to life.

Pity about the monitor it looks in great physical condition.  


Congrats again.

[gertsy]

A little more progress on this project, waiting for bits to come in from Newegg, AmigaKit, etc., is making me bite my nails, just have a couple easy questions:

1 - Thoughts on the GeForce 040 - should I run it with the little metal cover on or off?  I'm sure GVP knew what they were doing when they put it on there, right?    *wink wink*  Offhand I'm guessing better RF protection and lower noise on, but better airflow off.  Will probably go with "off".
..

Thanks!!!

Mine runs in cover off mode. I had to replace the fan and the new one was half a mill higher than the cover.

[gertsy]

......
Unfortunately it seems that even after cleaning the heck out of my motherboard and installing one of those AmigaKit coin battery adapters, it's not keeping time.  I can set the time and save it, but when I turn it off and back on again the time just comes up to whatever it was that I originally set it at (like it's stuck in the past), or occasionally some random time.  I'm going to try to check it a little more, but on the off-chance does anyone have a 6.4 or 6.5 motherboard with no battery damage they'd like to sell?  It can be completely stripped of chips because I've already got all those, but an undamaged late revision would be nice, or tips to repair this one?  I've got a spare 4.4 that works but would rather not step back to such an older one just for a working clock, LOL.    Thanks!!

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.

[gertsy]

I can see the Baking Soda (it's alkaline--should neutralize acid), but Vinegar or citrus? Those are, themselves, acidic in nature.

Maybe a little distilled water with the Baking Soda to make a paste and then gently clean it  (light scrub) with a soft, soft toothbrush.

NiCad batteries contain acid?  
Nickel Hydroxide plate, cadmium electrode and alkaline electrode. Not sure what's doing the oozing but it's obviously corrosive (oxidizes.) i'm not sure there's anything in there that's an acid though.
But baking soda is a great cleaner for acids or bases in any case and it doesn't stink.
As long as you remove any residue. Your teeth are a good example of how good it is.

@Zipper.  My experience with A2000s has taught me that sometimes 3v just aint enough.  But I'd check the RTC chip with a volt meter to see what voltage is getting to it from the battery.  As it might be the battery, socket, bad solder joint, bad track, or a partial short that is causing the problem.

[gertsy]

......
So with my multimeter I measured 2.9 volts directly between battery positive terminal and case ground, and 2.63 between R803 and ground.  If I understand correctly this is telling me I've got some degradation in the voltage along those tracks, but not much.....

Hmmm that's sus. If I get you right there's a drop in voltage between the battery and the RTC chip. There shouldn't be. The voltage should be the same at both ends of the track. If you can test the voltage at the solder joint where the battery enclosure positive terminal is connected to the track, that will tell you where the problem is. It's possibly a short on the track or something wrong with the Amigakit coin battery unit. (Could be the diode has fried from overheating).

Testing voltages with the power off isn't going to fry anything as long as you are careful with the metal probe points so that you don't short between tracks or components. Which is fairly hard to do but can be done if you're a little clumsy.