The 03/04 IRS has stronger half shafts, and some better subframe stiffening/reinforcing. Honestly, the 99-01 IRS is pretty weak, and wheel hop is a big problem. Using the 03/04 IRS is better, but it still has it's problems.
The lower control arms are the same. The hub/spindle assy is the same. The upper control arms, subframe, axle shafts and differanital are different. All the 03-04 stuff is better.
Small cheap upgrades you can do are to change the lower subframe bolts. They have 14mm holes in the bushings and the body, but Ford stuck 12mm bolts in them. I replaced mine and thought it took off a little smoother and stayed straighter. It also cut down on wheel hop.
The number one thing you can do no matter what year your car is...is a sticky tire. Buy some 275 Nittos. My 04 has NO wheel hop after that simple mod. They don't hook the greatest, 1st gear I can rip off with almost 600RWHP, but they make the car driveable that's for sure.
I will agree with the stickier tire up-grade. I put on a set of Bridgestone Potenza RE010s on my '99 and it really reduced the hop to almost nil. The hop issue has never been as bad with my '03. I use Cooper Zeon 2XS and I get good traction without having to go to the real sticky, low tread-wear tires. Virtually no hop plus confidence in the rain that you don't get with some of the real sticky tires.