ok a couple of things here, a bad water pump can cause a leak, but will not always.
where did the water leak out of the truck? this will tell you where to look, just because the coolant leaked out does NOT mean the water pump is bad.
a bad water pump would not cause it to run rough, but wet coils plugs or other sensors could
CEL codes will not tell you a cracked head or blown gasket
no oil in the truck can cause ALOT of problems including rough running issues, you may have destroyed your engine running it w/o oil or coolant in it.
overheating an engine (pegging the temp gage) is likely to have blown a head gasket or worse (cracked heads), you need to take them apart to determine which has happened, you can determine which cylinders have the problem with a compression test.