Yes I did, and mine does not have a LSPV. It is a 4wd w/ABS. In fact I bleed them 3x now. Once for the master cylinder, once for the calipers and once again for the replacement master cylinder. I'll do it one more time today for the new flex lines.

Yeah, any time you open the system, you really should bleed it out, again. It doesn't take even a single air bubble to cause problems, and a single line broken open to make an air bubble. Sp yeah, when you opened the system to replace the master cylinder, when you replaced the lines, etc etc etc. That's why you should try and do everything at one shot, if possible. Saves a lot of brake fluid

Good luck, and let us know how things work out for you
Pat☺

Success! At least I think so.
I replaced the flex lines today and took it out on the highway. No violent shaking like before, so for the most part I think it is fixed.
I am however having some doubts, I notice a mild vibration when driving normal. It may just be the age of the car, or it may be me being hyper sensitive to it since I was having these issues.

Thank you everybody who helped! This site is an invaluable tool to keeping our 4Runners running! Hopefully I have uneventful next 200,000 miles

Ball joints, bushings and other suspension issues could also be contributing.

-Charlie

Sorry but I claimed success too quickly. With everything I did the vibrations are much less, but my brakes are still dragging. I took a long drive today and it seems to get more noticeable after it warms up. The fronts are hot and they have fresh brake dust. Since the fronts engage first this makes sense. But I never adjusted anything linkage wise, I just replaced the master cylinder when it was leaking. The other stuff I replaced such as calipers, rotors and flex lines were after the issue became apparent to me. Being that I had two new brake master cylinders on it, I do not think that is the issue. Brake fluid flowed freely through the lines when bleeding so I do not think there is a blockage.
I am really stumped.

OK after watching a few more videos, I have it fixed. I wish I could rename this thread to help other people with the same issue. When I installed the new master cylinder (s) I did not check the length of the booster pushrod. When I replaced the first one I never checked it and it worked fine. Perhaps Aisin is making them with a shorter inner space, I don't know. This was off a few millimeters and was causing the brakes to drag and was also blocking brake fluid from backing into the reservoir.
After a road test, I have no more vibrations and I could tell instantly that it was not being held back.
Thanks again to everyone who helped out.