I was also involved in a 55mph head on in my 78 f150 so brakes are something really high on my list.
Never been in a major wreck due to brakes. Minor fender bender (no brake lights on other cat and my brakes locked up) that resulted in my front bumper getting bent (84 Ranger), but no damage to other car.
I'm with you on the brakes though. I learned about inadequate brakes on my dad's old 68 F100. That 390 FE would pull anything, but that doesn't mean it would stop it. The 4x4 and oversized tires didn't help either. That's why I start any build (actual or wish book build) by looking into what can be done for brakes and suspension, then I'll look into engine. IMO if the truck can't stop or handle the power there's no point in having the power.
The first step in building my V8, 2wd, 86 Ranger was to find the best brakes I could afford for it, then I went a step further. I've probably got about 3000 in the truck right now. $500 was the truck itself, $500 for the complete Explorer donor, and ~$500 bucks for miscellaneous parts for the engine swap. I have $1500+ in brakes and suspension, a thousand in the front brakes alone. The rear disks were free with the Explorer; and I'm not counting the upgraded sway bars, full poly bushing set, or upgraded shocks because I've had those sitting on the shelf for years for the truck I totaled. Just wish I had time/energy/motivation/weather to get all those parts installed.
I won't do any upgrades to the 99 though. I think it would be find with bleeding the system. Plan to swap back to stock size tires and sell the truck in the next couple years, so I'll spend enough to keep the truck safe and road worthy, but no more upgrades unless it helps sell the truck. Engine is getting tired and I'd rather get (or build) a full size than dump the money into rebuilding this engine. Want to build dad's old 68 since it's been parked for years. First step on it if finding a replacement body. Then it'll be finding out which late model super duty solid axles with 4 wheel disk brakes will fit under it and fit properly. Drop it back down to just high enough to clear 31-33 inch tires, don't need a lot of articulation around here. Beef up the motor, bump up compression, aftermarket heads, and swap in fuel injection. Then find a 5 speed manual with extra low first and overdrive.