93 Suburban 1500 Silverado 2WD 5.7 brake question

I found out that the master cylinder was empty on the back part of the res when I bought the truck which explains the dismal brale performace and long pedal. I got it home safely and filled it with brake fluid and bled the 4 brakes but still had a spongy pedal although not as bad of course as when I 1st tried the truck. I noticed a violent swirling of the fluid in the res. When applying the pedal and since the res. Was fillthy with brown sludge when I first filled it I decided to just replace the M. Cylinder. I bench bled it first. I still have swirling going on in the new m.C. Res. And the pedal still travels too far for my likes. What did I do wrong or is the early abs, the booster, or something else at fault? Regards.