I definately recommend doing the 4.10 gears. Howerver, even a mechanic that has worked on transmissions and diffs for decades may redo the gears a couple times before they are completely happy with them. I don't know that a tech article would be very helpful. Part of it is experience. I take my Jeep to one person for this type of work. He did my gears, converter, and shift kit. He fixed the damage that the dealership did to it also.
Now that you've gone to 4.10's, you need a Fastman throttle body and a B&G flash. You will be pleasantly surprised. My Fastman throttle body made the most seat of the pants difference for the money out of all my modifications. The B&G flash is worth it for the torque management deletion alone.
If you've got the 42RLE, you should really start talking to people about a better torque converter. You're loosing a ton of power there. You will also need to try to find a shift kit so it will shift quicker, and it will increase the line pressure and help it lock up better and slip less.
If you're lucky enough to have the 45RFE, just call APS and get the torque converter and performance shift kit.
Everyone will swear you have a V8 in it.
Edit
Almost forgot, your computer won't completely figure it out with resetting it. You need to disconnect the POSITIVE cable from the battery. Turn the ignition to ON. Do not try to start it. After 15 seconds turn it back to OFF. Then reconnect the POSITIVE cable. Over the next 50 warm up cycles it will retrain the computers.
Edit
Make sure you have the NEGATIVE cable disconnected from the battery prior to doing anything with the electrical system. Reconnect the NEGATIVE as the last step.