420A hesitation / miss in 4th & 5th gear

[mic]

420A 2g GS just got back on the road.
Had motor rebuilt, new clutch, axles, etc.
Came without the factory air box. (K&N CAI instead.)
Did not have the problem before taking the car off the road for rebuilding the engine.
Changed plugs to NGK Iridium, and it seemed like the hesitation went away.
The next dayit was back.
Idle is fine, but it has shut down on me a few times for no good reason. Other than that, it runs fine up thru third gear on a 5 speed manual. Once you hit fourth it feels like it is hesitating or missing.
Vaccum hoses look fine, but will replace all since its a cheap fix.
Tried changing out plug wires with old set and it made no difference.
Not getting any codes on CEL other than the dreaded pulsed air injection thing that I will fix with a resistor in the PAI plug.
Anyone else ever have this problem that would save me testing and guessing by throwing parts at it?
Thanks in advance.

 

[mic]

Replaced all vac lines. Alternator, plug wires and coil pack checked good.
It's either an emission sensor or fuel system problem.
Since it is not showing CEL, I will focus on fuel system.
Fuel filter has probably never been changed, so it would make sense to start with that.
Tried to buy one at Advance Auto, but they did not stock it. (go figure)
Will try Napa or Pep Boys and report back.
Also, drained out break-in oil and filled with Mobile 1.
Side note just to start a fight, tried to buy OEM gear lube for manual transmission. Both Dodge dealer and Mitsubishi dealer told me they could not help me. (Actually Dodge told me to go away, and Mitsubishi told me I had to buy it by the case, because they didn't want to stock it at $15/quart and be stuck with it on the shelf.)
Tried to buy Amsoil, but got creeped out by the "local dealer" mail order thing where some dude ships it from stock in his basement.
So, it's Syncromesh for me. nuf said.

 

[mic]

No ideas guys?
Bought some seafoam to try to clean the injectors / throttle body. Doubt that it is a fuel problem, because it runs great thru third gear.
Very strange. Strange and frustrating.
ECM anyone?

 

[1MeanTSI]

Your trans could be going. Also where its a lot taller of a gear, your motor is under more of a load. Your fuel pump could be going. Does it buck or stutter?