I have searched and read through a lot of posts, and have tried a lot of things, have also had the car at a reputable shop and still haven’t been able to solve my long brake pedal throw problem. The car stops well, but the brakes don’t engage until the pedal has traveled a long way. My car is an 89 with a 9 bolt rear, ls1 front brakes, pbr rear brakes, third gen master cylinder (have tried both third fourth gen), gutted proportioning valve (tried three different disc to disc ones), braided brake lines, and a fourth gen pedal set (6 speed conversion). Parking brake is correctly adjusted. From what I can tell between all of the threads, the only thing I haven’t tried is upgrading the rear brakes to something else. Are there rear brake upgrades that resolve this? Any other ideas to resolve the issue?

I do know that our third gens came from the factory with basically non functioning rear brakes due to proportioning valve design. In my car (which was originally drum, now disk rear swapped), the rear brakes appear to not even engage. I know this because they are not wearing through the rust on the rotors, while the front pads did so immediately. So I am putting in a heavier weight spring in the prop valve.

Upgrading your rear brakes will not likely solve the issue, as your brake system does not "know" what type or size of rotors it is using. It is simply applying pressure to fluid. You have an issue somewhere else. I see you say braided lines, but could they have collapsed, pinched, or been twisted? How sure are you that they are properly bled? That pedal swap seems suspect, as in a physical linkage problem under the dash. When you grab brakes quickly, do your hear a swishing sound of air, or do the brakes feel spongy? Or does your pedal feel firm and the brakes work well, but there is just an inch or two of "nothing" in the pedal travel?

I understand that changing the rotor size will not impact brake application issues. Looking thru many of the posts of others having the same problem, the common thread seems to be that nearly all of them have PBR rear calipers. Once I got to a point I was running out of ideas on this problem, I took it to a reputable shop run by a guy that used to be the lead mechanic for our local Sheriffs dept. He worked on it personally because the problem perplexed him as well. System was vacuum bled several times. He tried both third and fourth gen master cylinders, and we went through 3 used or "reconditioned" proportioning valves before he gutted one. Car stops very well once you push the pedal through the dead spot at the top. Firm pedal, fronts lock first, rears lock if you stand on it. The brakes lines are brand new and are either earl's or russell, can't remember. Not twists or kinks in any of the lines. No air noises on hard application of brakes. Current PBR calipers are both fresh rebuilds and the parking brakes are adjusted correctly (that does make a difference on those calipers - by getting adjustment correct, we were able to get the rears to lock under hard braking) Because of that, I am wondering if a different brand or style of caliper may make a difference. If the PBR retracts too far or the piston is too big, it will take more fluid to move it, which could contribute to the longer pedal throw. Just looking to see if anyone has tried that solution and what their results were.

have you checked the pushrod between vacuum booster and master cylinder? maybe its not long enough and needs to be longer if not engaging the master cylinder as soon as you start pushing on the pedal?

If everything feels good with just a dead spot at top of pedal then there is too much space between moving parts somewhere. Linkage at pedal, pushrod to master, pistons retracting too far. Something has slop. Most likely it's somewhere in the pedal and booster pushrod.

It does have a stock length push rod, but that is something I have not checked

The clearance should be very small. I can't remember the spec off the top of my head but I think it says in a tutorial at the Master Power Brakes website. There are specialized tools that help with the measure such as Master Power Brakes part number AC2003.