Keep it simple.For the rear reinforce the rear trailing arms with a boxing kit, change the CV joints to Type 2 or Type 4 ( Type 4 having more degrees capability) You will have to change output flanges on the trans and also the stub axles but either is no big deal. Add a GOOD shock. Weld up the seams on the rear frame horns put in good transmission mounts with a strap kit. Fab up a skid plate and rear bumper. You will need a simple roll cage to tie the rear shocks into.
For the front weld up all the seams on the BJ front end, replace the balljoints with good ball joints add Class 11 shocks( fox, bilstein, etc,) reinforce (sleeve) the tie rods, or replace with HD, replace tie rod ends with stock, aftermarket Ford or International or hiems, set up a hook and rod set up for travel stops, reinforce the steering arms,put a shim between the pitman arm and the bottom of the steering box, leaving approx. .015 interference. Remove front sway bar. Fab up a skid plate and bumper.
Buy the book Baja Bugs and Buggies by Jeff Hibbard. A bit dated but full of tips on building simple bajas and buggies.
You will be amazed at where a simple baja can go:Wow1: