It is possible a valve stem seal is leaking. Puffs of white smoke would be the indicator and account for OIL in the intake ports you photographed.
Tough to say, without testing. Let's hope that is not the issue?
A pressure leak down test would be required to investigate a valve stem seal leak, after you see oil or white smoke puffs in the exhaust.
Before you can test, you need to verify valve lash is 100% to spec.
Perhaps you could concentrate on the manifold leaking with the explained bolt torque weakness?
The problem with what you describe, loose hardware, is the possibility of air infiltration into the manifold and causing a lean condition, anywhere the excessive Permatex caused a poor seal.
How about verifying the rocker arms are exactly the same tension and the valve lift is not compromised with a worn lock nut or two?
Rocker lock nuts and the 3/8" studs, can and do get worn out and cause bent valves because people are afraid or not trained to re-set the lash to spec.
It is possible one or more valves have been running with improper rocker adjustment and caused a leaking valve stem seal.
Let's hope this condition has not been beating your cam and roller rockers to death.
Your pictures of the fuel/oil or coolant will tell you where to check for sloppy rocker adjustment. Remember, they are opposing tunnels...
Check and adjust them all. The bump switch will make this easier. Please disconnect the battery negative before wiring the bump switch?
The GM Dealership 99' service manual for the 5.7L (using a stock roller cam) calls for "1 additional 360 degree turn after lash is removed".
Page 6-208 Engine Mechanical 5.0L, 5.7L
(IE: the push rod cannot be moved up or down and rotating is just possible and not restricted).
***This is NOT the process for a flat tappet camshaft on a 5.7L***
If your seal got beat up, you'll know when the valve lash is way loose and the nut requires more than 1/2 turn to correct lash.
This will indicate the lock nut or the threads on the stud are worn out. You can crush the lock nut in a vice to temporarily fix it.
If the stud is worn threads, it will be OK with a slightly crushed lock nut. New lock nuts might still be loose if the threads are beat from loose rocker lash. You'll be re-adjusting exactly where the poor threads are when you tighten to spec.
Threads might be beat exactly where you need to be, when dialed in with the 1 full 360 degree turn, after zero lash.
Oil on a plug means oil bypassing your rings or bypassing your valve seals. Oil can bypass a working seal if the stud threads are worn and the rocker is hammering the seal. (I know I already said this, but it needs to be said again). Let's hope it is coolant and fuel from the leaking gaskets and loose manifold bolts.
If you find this situation, where the rockers are loose and lash is off the chart, prepare to remove a spring or two on the heads and swap a seal or two to correct the leak before you move forward. If you are certain the valve seals are OK, then a leak down test will inform you of a bent or leaking valve. This occurs due to loose hardware, leaking gaskets, leaking seals or all of the above. You may have a crack in the head leaking oil or coolant or both. Leak down test is really what you want to do.
I'll mail you my OTC Leak down test kit, if you want to borrow it.
You might find fixing the manifold gaskets gets you running.
Adjusting lash after this issue will safeguard your engine and inform you what else might be loose.
