Love my Baja...
About the best farm car you can ask for...
A few things I've learned:
1) King/Link-pin front suspension > Ball-joint front suspension
The ball-joint front suspension (late model) will hold up for a while with light use, but the King/Link pin suspension (early model) is damned near indestructible. With adjusters of with the "cut and rotate" method you can get up to 6-7 inches of suspension travel. With a decent set of shocks, that's more than enough to get in trouble.
2) IRS/Swing axle = User preference
I prefer the Independent rear suspension, but others may prefer the swing axle. Both are stout enough for light abuse in stock form.
3) Get a body lift and a roll cage
The body of the bug can be separated from the pan quite easily. Many companies make body-lift kits in sizes up to 3 inches. The kit bolts in between the body and pan, and provide you with a little more travel before your gigantic tires hit the fenders. Rollcages are cheap, and many simply bolt in, although it's recommended to tie the cage into the frame horns. The big-boys buy long shocks and bolt the upper mounts on the cage inside the car.
4) Get a bus tranny
A 3-rib bus tranny will bolt in more or less, with the caveat of running the shift linkage above the tunnel rather than below it. They're geared better for big tires and take the abuse better than a bug tranny.
5) Steering Boxes are $60, buy two.
You'll wear them out quick...
6) If you catch air, push the clutch in and hold it 'til you land.
You'll break the transmission if you land with the power-on/in-gear. PUSH IN THE CLUTCH!
/Mines for sale, but it's just a bit over the $2008 maximum