2000 Ram van 3.9l overheated and now runs very rough

Several things

1. 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.

2. 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 time and watch for bubbles).The head gasket seals the coolant from the block , when you overheat the engine the big metal head warps which breaks the seal on the gasket and lets water in.If this is case , its a new head replacement(buy new car ,expensive work)

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 from the radiator:

• When the engine is cold (cool not freeze)
• open the radiator cap
• fill in the water/coolant until full.
• Preferably 2 persons doing it, one to look at the radiator and the other cranking the engine.

If the radiator shoots the water out when cranking it, your compression is leaking out to the water inlet/hole that's why the water shoots out to your exhaust.

Another one is to check when it is running if there is any leaking water from between your cylinder head and engine block (see the head gasket line). If there is leaking water or like a bubble coming out from the head gasket line your head gasket is blown up or worse your cylinder head is wrapped.

If the cylinder head is wrapped you don't need to buy the new head, you just need to resurface it (resurfacing), just go service shop that have a resurface machine. Or you can go try to resurface yourself, which using sandpaper, there is plenty of youtube video how to resurface it, I have done it myself, but better use the machine because it makes me exhausted resurfacing the iron cast head :)

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 troubleshooting any further.