I got lucky and picked up a jeep cherokee for $500 that was flooded in Katrina.
The only thing wrong with it pretty much aside from cosmetics, was that the starter had gone under water (saltwater) and it was rusted up solid. The owner tried to crank it and hten sold it to me with my intentions of parting the thing out...
after some looking around on it and realizinf hte water only got a few inches in the floorboard, I swapped on teh starter and battery from my other jeep, checked the engine nad trans for water intrusion (none!!) and then tried to crank it.... fired right up!
I put a new starter and battery on it then, new tires, new brakes (they were rusted up well) did a full tune up, and a few other minor things, installed radios and laptop desk...and I've put 10k miles on it already, it's been on quite a few chases (did lose a brake master cylinder on one chase)
Over all it's been a good investment. If it lasts me 10k more miles i'll have definitely gotten my money out of it.
The thing is, I do all my own work, and I know jeeps really well since I have a wrangler that is my trail rig.
On your jeep, it's chaseable, I chased in my wrangler a little when it was my daily driver. the 2.5L jeep engine is anemic at best though. I'd go with no more than a 31x10.50R15 tire at the very most with stock gearing and that engine.
Get the exhaust manifold leak fixed (replace it with a good aftermarket header, welding the factory one is pointless, it'll crack again.)
I like the hail shield idea, as large hail can punch right through the hard top... one thing though, you are lacking the lightning protection factor of a metal hardtop. an overhead roof rack grounded into the body, while reducing gas mileage slightly and increasing road noise markedly, it could offer lightning protection.
Those engines are fairly reliable though, give it a good once over, new belts and hoses, new radiator, water pump and thermostat, spark plugs, wires, cap and rotor, keeping all the old stuff as spares.
if you have a manual transmission, its is likely the AX-5 that is an extremely light duty transmission... 5th gear is known to go out...if it does, dont worry about it, the gear actually falls right off the counter shaft. it'll get you home, get it fixed then.
anything else, just ask. feel free to pm me.