I did the zj swap on my 98, no booster change + bled the brakes really well.
At first it was unimpressive, then it was inconsistent, then it worked really really well. Seemed to take care of itself right up until I blew a rear brake line - fixed that, bled it, it performs great.
I wonder if your booster is causing the inconsistency / problems. Don't know a ton about them but you've changed three things - the problem is in one of them.
Did you use new calipers?
Are the bleeders at the highest points?
Are you sure the system is air-free?
Have you tried going to OEM prop valve or otherwise troubleshooting the prop valve?
After that.. its the booster. I'm rolling on ZJ discs, cheapo pads / rotors and have awesome braking performance. No reason you shouldn't be better off.
But like I said - I had mystery issues for a coupla-few thousand miles before things seemed to settle in and perform consistently well. To this day I don't know WTF was going on.
EDIT: Also. Check your pads for glaze or abnormal shininess / wear. I wouldn't mention it but I put a solid glaze on my front pads about 5 months ago and wound up replacing them. Made a HUGE difference, even just buying cheapo pads. If you use the brakes on a long downhill (like we tend to get out west) you'll quickly burn up the brakes and even boil the brake fluid, causing sponginess in the pedal. Put the trans in a lower gear instead - I put my AW4 in "3" and it never breaks 53 MPH. Sorry if this is a "duh" but I grew up in Maryland and had to learn this the hard way out west.