First one: stock or after market knuckles?
Looks like the previous owner had broken a knuckle stud and just filled the hole/void with RTV, idk if this was out of laziness or the threads in the knuckle are stripped. Haven't pulled and cleaned it up to see/replace. I plan on rebuilding the knuckles this fall so do I just find a factory knuckle and upgrade it or go to a 6 stud and be done with it
6 stud knuckles is a bandaid. studs break because of movement in the knuckle that putting side load on the stud, snapping it off. 2 things that help with that: first and most important, just check the torque on your steering arm nuts occasionally, should be around 70 ft lbs. Second, as toyodaaddict suggested, 25mm pins. The larger pin and bearing, help eliminate some of the side to side innate motion in the knuckle plus is just larger stronger pin. Given the 6 stud arm can apply more pressure through 6 studs to help keep the arm tight, but still needs to be checked for torque, and only uses a 17mm steering pin.
Second: PS pump.
This one is a quick one. On 37s do I keep the factory style 88 IFS PS pump or replace it? Thankfuly the truck already has steel PS couplings and a nice HP line, with a cooler.
Stock pump with a cooler should be fine. Thats what Marlin, Mike and most other people at the shop use, and have no problems. If you are looking for an upgrade, PSC makes a High Output Pump for a little more pressure, but as long as the pump is still working good I'd just leave it.
3rd and last: Break MC
Yes. The FJ80 brake master cylinder is a great upgrade. But it has to be the right FJ80 Application, the US model FJ80 brake master cylinder has a different electrical connection. the proper one can be found at https://www.marlincrawler.com/brake/master-cylinder/big-bore-fj80-brake-master-cylinder