2.5L is experiencing rough idling conditions, sometimes jumping in rpm or falling to 400-500 rpm and struggling after hitting the throttle. It also backfires while in gear and engine braking (not pressing throttle but under load), and sometimes backfires after hitting the throttle while not under load.

Just bought a B2500 and I am overall pretty unfamiliar with this engine so any help is appreciated, here is some background info:
Mazda B2500 with a manual 4x2. Body has 140k and a new engine was put in at around 100k, with several new components.
When I bought the truck, it was running rough with cly 4 misfire and lean code. I was told it was a bad injector, so I replaced all 4 injectors. which cleared all check engine codes.
Then I noticed "spark leak" or arcing off the plug wires, so I replaced all the wires and plugs (some were in rough shape). Still ran rough so I investigated and noticed cly 3 on the secondary coil pack (intake side plugs) was not sparking, so replaced that coil pack as well (but not the primary one).

Now mainly suspecting a vacuum leak? I found one of the red vacuum hoses from the throttle body was disconnected by the solenoid (where green and other red connect) and the vacuum reservoir is completely missing. I plugged that line and no change.
Started to try and do a smoke test on the vacuum system and found it was leaking from the IAC valve, but after some research I think that is normal? (please let me know if not I got conflicting information so far).
Will the missing vacuum reservoir cause this? From what I have read so far it is mainly to help with the climate controls in the cab.

If anyone has any helpful leads on how I might fix this please let me know, it has been driving me crazy.