I suggest reading some more. I've had mine rooted two different times and running Honeycomb simply by following the instructions listed in the above forums. If you don't find the solutions there we may need some more details.
Android is a linux operating system. If you're so savvy with computers, shouldn't it be a breeze? ;-)
Anyway, how do you know you are losing root access? I've never seen that happen to me. If you open something like titantium backup or some other program that requires root (such as SetCPU) what happens then? (or I guess the savvy can open up a terminal window and then try to su)