Hehe... don't confuse "educated and working" with "expert"
I will be proud to help this project in any way i can. You have accomplished an amazing amount without any embedded systems/electrical engineering background. Good work!
Quite frankly, you don't need to sample the A/D converter that fast... 100Hz would be fine.
Watchdog timer was an obscure concept when i started this stuff. It is actually quite simple. You enable it, then it counts down till it expires and resets the chip. The idea is that your code will regularly reset the timer so that the chip doesn't reset. If ever your program hangs due to an unforseen bug (it happens to the best!) your system resets and you carry on with life. Ideally, a watchdog reset would be followed by an immediate shutdown of the motors.
In my reading, the big risk with DC motors is the ability to run away at full throttle if your control goofs up. I'd do as much as possible to ensure that this doesn't happen... just keep it in mind, don't hang up your project on it.