I put new thermostat on and it started running very hot again. I drilled to holes in the thermostat to increase the water flow and it still ran hot. It's weird cause the bottom radiator hose was running very hot and the upper hose was ice cold. So I thought there was a clog somewhere. I flushed out the radiator and the heater coil and water was running through everything. I hooked everything back up and put thermostat back in and was running hot again. My buddy went to take the top radiator hose off the thermostat housing and there was so much pressure that the coolant and water went everywhere. It runs just fine without the thermostat but I'm wanting some heat now. So my question is.....Could the new water pump you installed be bad or could there still be a restriction in the radiator or heater coil? I'm asking cause when the thermostat is out and the Jeep is idling the temp is at 210 and when I'm driving it drops all the way to around 100.

Flushing a radiator at home is most often a waste of time. The chemicals used by a radiator shop are far stronger than anything you get at the parts supply house. What happens is that the flow you see is deceptive as the water tends to flow around a partial restriction and does nothing to remove it.
Though your garden hose has a lot of pressure it doesn't have the volume necessary. A garden hose will usually be sufficient to flush out a heater core though as it's smaller.
Have a radiator shop flush your radiator core and have a hydrocarbon test done on the cooling system to eliminate the possibility of head gasket problems. When re-filling the system, turn the engine off just before it reaches 210 degrees and let it sit for a few minutes so the thermostat can open, then continue filling. Always fill with the heat on high. Thermostat goes in with the spring end into the engine.Forget about the water pump...unless you got one made for a twin engine marine (CCW) application it has nothing to do with the problem though I've heard but never actually seen that the belt can be installed so it turns backwards.
When the engine is at operating temp cover the grille and force it to nearly go into overheat...the electric fan should come on and the mechanical fan should lock up to try to counteract that.
Don't open the system when it's hot (you found that out already). And, don't allow the engine to actually overheat.
My bet without seeing it? Likely a partially obstructed radiator. 4.0 engines make a lot of rust residue even when maintained. If that's what you have in there, or even the 4cyl. It is more than likely.