I am currently having transmission problems. One day, all of a sudden, I had no overdrive, and realized I also couldn't shift down into 1st gear or upshift from 1st. I believe I have 2nd and 3rd gears only. I know my transmission itself is not the problem, the mechanic said it is a transmission sensor or a solenoid that needs replaced, not the transmission itself. Since my mechanic is experienced on the subject, and happens to be my brother-in-law, I trust his opinion.
A lot of people with the same issue have gotten bad advice and replaced the transmission, and find out the problem still exists. Simply put, not checking solenoids and/or sensors first can be a costly mistake. If you don't have the typical transmission problems such as gears slipping, no gears but reverse etc. it may not be a bad tranny, just bad parts associated with it.
Don't hesitate to question a mechanic on this subject, it might save you from fixing something that isn't broke, saving you a pretty penny which will come in handy paying for all those parts that consistently rot away and fall off at the worst possible time.
To disarm the alarm system without remote, you have to use the key on the PASSENGER side door and turn the key to the unlock position 2 times. Disconnecting battery or other wires might shut it up, but it doesn't disable the security feature that doesn't allow the vehicle to start if the alarm has been set off. If you do what I said, it should disarm the security system so the vehicle can start.
Do a little research, and you'll find that JC's have some type of liner or coating on the inside of the gas tank, that turns to crud and debris that eventually ends up in fuel filter, fuel line and other fuel components, causing the exact same issues you now are having. Finding someone to clean out your gas tank the way it needs to be isn't easy. Might need to just replace gas tank with the crappy liner or coating that's causing the problems, to prevent future damage on your engine.