97 4.2l rough idle/miss at all rpms
 

Hello folks looking for some help here. A lot of information to share, so if this is lengthy, I apologize in advance. Just trying to give as much info as possible.
I have a 97 with a 4.2l with 110,000 miles on it. This is the trucks second engine. Issues started about 2 months ago, the truck started hemorrhaging oil from the front of the engine. Took it to the shop and their Ford mechanic said it was leaking in several places, but the main culprit was the front seal. I had them replace that, and all was well for about a week, then it started all over again. It appeared to be pushing out around the timing cover, and through the timing cover bolts. Was told it sounded like the PCV valve was not working correctly, causing pressure to build up in the crankcase. Replaced the PCV and cleaned all the vacuum lines. It didn't help. Also noticed oil on the filler cap was "milky", so I thought maybe head gasket, since this engine is notorious for that. Checked (and changed) the oil in the engine, no sign of milky oil in the oil pan. I took the truck back to the shop that installed the engine, and they replaced the timing cover and gasket. Engine still leaking oil. Then last week I had an issue with one of the freeze plugs blowing out so I decided to just bite the bullet and have it all done, head gaskets, freeze plugs etc.
The truck ran smooth as silk despite the issues, however now it runs like crap. Computer(not one of those Autozone types, mechanic had one of those SnapOn high dollar ones) showed that the butterfly valves in the intake, bank 1 was stuck open. Mechanic removed the plenum and discovered the linkage was disconnected. Fixed that, put it all back together, and started it. still missing/running rough. Computer shows only that cyl 4 has a slight miss at idle, but zeros out at higher rpm. No other codes.
Problem is that the truck still runs rough and has a major miss at any speed.
02 sensors have been replaced, new cats, new coil, new wires, new plugs. EGR ports were clean. New EGR tube. Although there is a "hiss" like a vacuum leak somewhere, all lines were checked, double checked and triple checked. No sign of vacuum leak aside from the hiss. Plug wires are on the proper plugs, not miswired. I need some spit-balling with this as the truck is not really drivable now.:confused::help::mad: