First I want to say this is a great site That is full of information and thanks for having me. Now for the Nightmare I own a 1998 4Runner 195,000 miles on it. Has the v6 motor. It all started with the passengers Wheel Bearing being bad. Had rear end fluid all over so I replaced both sides everything Bearings, Seals, ABS Gear,O-Rings, Brake Shoes and Wheel Cylinders and Bleed and adjusted brakes. After replacing all that the brakes did not feel right they were going to the floor so I went ahead and bleed them and they still didn't feel right so I replaced the master cylinder and did re-bleed which helped a lot but they still don't feel right. Now I can drive it and stop good but the pedal seems to go down to far but not to the floor. I normally don't drive this. Is it because it has drum brakes in rear and it don't stop as good as Disc ? I normally drive a 2007 Fusion which has 4 Wheel Disc Brakes

 

Are the rear drum brakes properly adjusted at this time?

Welcome to YT!

 

Number one suspect is that there is still air in the lines.
Number two, as has already been suggested, is the rear brake adjustment.
It could be a very tiny bit of air still in the rear lines that'll give that "not quite right" slightly soft pedal feel.
If you are tired of the bleeding routine, find a small, friendly, independent service/brake shop, and ask them to do a quick brake bleed. The place near me did it for free...it took them about five minutes. Way faster than I could have done it myself.

 

Thank you for the help. yes I did adjust the brakes so there was just a little drag when spinning the wheel. I think my next step will be to take it and have them do a brake bleed. Another thing I bought my shoes from Autozone maybe I should have bought OEM from Toyota ? and one more thing I notice when replacing the master cylinder there was a gasket between the cylinder and the booster the old one looked bad but they did not give me a new one with the new master so I used it anyway.

 

It can be hard to get all the air out. Especially if you get air in the ABS modulator unit.