A vacuum valve broke and you replaced it with a straight pipe? You likely have a large vacuum leak (or imbalance), especially since your brakes are "mushy." Vacuum lines that are hooked up incorrectly can definitely cause a loss of power, stalling, "Check Engine" light and other problems. Replace the vacuum valve properly before ...
The fuel injector couldn't get water inside since the fuel line system is using a different line system.
Like binaryOps20 said you could possibly damage the head gasket because there is excess water shoot out from your tailpipe.
How to check blown head gasket:
Use the blown head gasket test kit -Like this one-
Check with your radiator.
Another to check ...
Could be water in the intake resonator from that incident , remove intake resonator(box connected to intake hose) and drain it.Water will mess with air fuel reading and make idle crap.
You could have possibly damaged the head by excessive heat , try to do a head gasket test, (use dye kit or when engine is cold open radiator cap for a short ...