I agree, the brakes should function normally with out the abs fuses. One thing though, is your resivor (brakes) look like a big tylenol capsule. This would be the old abs system, pretty mush useless! I had this system and converted to the regular brakes and booster, minus the abs.
Ok, this may be out in left feild, but on fords and chevy's you have to do a service bleed on the abs system after you flush the lines, this is to get the air completey out, and if not done will give you the problems you are experiencing. This type of bleed is primarily done at the dealer or maybe by some one with a good snap on scan tool. Look into this, befroe you start to spend money. Go back to the garage you had the work done, and demand they fix your problem!Especially i all was working correctly before the flush.