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1999 Drivetrain in a 2001, What am I Missing?

I would definitely go with the Viper coil. I have one that I haven't installed yet but I can tell you I hate the coil rail. It makes reading the plugs and diagnosing a cylinder problem a royal BITCH!

You may get away with a Viper coil in Arizona but in California, having the wrong air intake hose can disqualify you. Both of my Jeeps have failed for insignificant "equipment" violations so I now make sure the engines look completely stock before an inspection. Much depends on how sharp the inspector is.
On my 2001, I considered the Viper coil when changing to the 7120 head but decided to stay with the coil rail to prevent inspection issues.
Other than making the replacing spark plugs easier, I couldn't see any real advantages and I didn't want to chance being caught by a knowledgable inspector....again.
Pulling the coil rail was made easier by extending the coil's wires by about 18", so it can be pulled out of the way without messing with the coil's plug.
 
Got the motor prepped to swap this morning, the header was a pain as expected but the harness went smoothly. Got a couple broken connectors that I'll have to grab from pullapart and swap out eventually and was missing the little capacitor thing the 2000's use. Got everything dropped in 01 after lunch and mostly finished before it got dark. Just need to bolt up the downpipe/mini cats, stick a driveshaft under it and finish off the front core support/header panel.



Thanks for all the advice everyone, it was much appreciated and the swap really couldn't have gone much smoother!
 
Our emissions test consist of visually verifying there are cats in place, readiness monitors set and no OBD codes/CEL. They also verify VIN on ECU to vehicle year model.

When you go for the smog test, make sure the air cleaner and intake hose are the Factory pieces, I recently failed a visual by not having the stock air intake hose. Luckily it was a ten minute drive home to grab the intake from my other XJ. The inspectors have little discretion when it comes to emission equipment compliance. I asked if a different air cleaner could be used, he said only if it has a CARB sticker or number.
The bottom line, keep it stock looking until it passes, then you are good for two years.
 
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