I'm still open minded.
Since I opened this thread I've put the iPad back to stock (as suggested above) and will re-jailbreak by adding just the tweaks I really need and see how it goes. That way, I might even identify what it is that causes the crash.
Thanks for all the comments and advice.
You might also try using Crash Reporter to symbolicate the crash logs, it works SOMETIMES, it's not perfect.
I would advice against using any "Battery *" logger on Cydia as I had a couple crash my iPhone constantly, removed and they showed to be problematic.
Also and as much as I've heard this advice, I'd install 1 tweak at a time, use the iPhone for 1 or 2 days then if nothing happens with regular use, move on to the next tweak, otherwise like in your case, I have too many tweaks and finding a culprit is a pain in the ass.
With the checking of the Crash logs you can see which tweaks or mobile substrate add ons are mentioned the most, then take your chances with Springtomize (I think SBSettings does it as well, but not sure as I don't use it) to disable some MobileSubstrate addons and see if that changes anything.
And if you have OS X, you can always try Xcode and running a session of Instruments to see memory peaks and the like.
Anyway I'm no expert but those are the things I'm trying right now and so far it's worked, I get less crashes that before, still I think there are a couple tweaks that I have to disable, trying to find which ones (and too lazy to restore obviously, plus it's more fun to chase stuff this way, you learn a lot more).
When you ask your phone to run an app that wasn't meant to be on it, with software that apple didn't approve, you find yourself running on hope and trust. It's a tradeoff you make to run fancy apps.
Yes, true. Hopefully a lot of tweaks will get included in the next iterations of iOS.
As for theming I just dropped that "dream". Winterboard themes just look cheesy to me and I'm just using it to theme the Lockscreen with a real slick-looking theme, that's it.
Can anyone here tell me if there is a cydia app that will show us crash logs? Something a normal person could deceiver? Even a processes/CPU tracker? My 3GS gets slow at times and I can't pinpoint it. With a restart and all apps closed its confusing to know where to start troubleshooting.
You posted while I was replying but I think I covered those two.
By the way, with BBSettings, you can see a list of running processes along with memory use (which is sort of like the unix tops command but in your notification center and without resort to using the mobile terminal, which can be clunky at times).
Oh and the "something a normal person could decipher", well, I think the crash logs while meant to developers, are not that hard to read (I'm pretty technical myself, being a CS, but anyway, I don't think it would be hard for the average user to read).
And you can also use iFile to pinpoint /var/logs and check Apple's ones.