Shuddering, 2200rpm 3rd to 4th gear

My XJ is an hypochondriac.
Or my problem child i'm not really positive yet.
Bought my Xj in 2011 with 153,000 on her.
Anyway 30,000 miles later Engine went, she has since been on a tirade.
I have had her going maybe 3 months out of the last 12-26. The place that I had swap the engine effed up my world.
When I left the shop they didn't even have the engine mount bolts in... I should have figured it out then :bang:

A week later the harmonic balancer went.

After some arguing about what the warranty on parts and labor covered, I got wise that the shop didn't have a clue WTF they were doing it I started redoing everything myself.

Since then the more significant stuff I've done has been:
Torque Converter
Transmission
CPS and TPS
Waterpump
Last was my personal favorite the Flexplate (You can see why in the pic below)

Anyway, last night she started being a dbag.
At around 2200 RPM 3rd to 4th gear the fuel cuts off and the engine starts shuddering. No backfires like I've heard of happening. If I let go of gas it stops, try to accelerate more she can sometimes jump up to 3,000 but mostly she just wont go until I let off the gas. Also been smelling rich. I'm assuming its misfiring.

I'm hoping that the Spark plugs being replaced (they were awful) will do the trick but just in case, am I overlooking anything? Any other insight on what I should check next or if there's some underlying issue I could be missing?

Any input would be awesome, I just want to get this thing working RIGHT and stop secretly expecting detonation every time I turn the key. :pray: