That was old news. That was on the cheap OBX LT's.
One guy from Hawaii did it few years back and he had to do that and relocate the O2 sensor bong and passenger side flange didn't line up.

The JBA LT's on another hand fit like a glove.
no issue with the O2 sensor locations. i used the upper factory locations. and plugged the collector flange O2 locations. i wish i could have used the collector location but i did a lot of reading and they say that if you extend the wires you will not get the correct Sensor Voltage reading.
there is plenty clearance on both sides of the headers. and i didnot have to do anything to the exhaust since i already have rotated my flanges when i installed the Berk B pipes and custom made SS cat back system. so everything bolted right up.
I wont say it was easy. it took me and my friend mechanic with his bay and lift and all his tools 1 and a half day to get it all done. sure i used the moment to change to H&R springs and Rancho struts as well. but i figured that would all have to come out anyway to get to the headers easier.
took off the engine and trans mounts. and cross bar, and front differential and drive shaft.
here are few pics of taking stuff off and supporting the engine and trans.
I will make a new post with pictures of install.

Pretty slick, forgottenzone.

What sort of tuning is http://uprev.com/about.php capable of? Is it an ECU reprogram or something that can be toggled back and forth like BullyDog?

UpRev is fully Reverse Engineered ECU Software that reflashes the ECU/ and then you modify it with your computer, if you buy tuner version $700. or if you buy a version to get it done by Etune $500. where you record data from ECU with your laptop. send it to uprev or a tuner dealer and they modify it and send it back to you and you program it back to your ecu.
or the cheapest $300 you can send your ecu and they will program and send it back to you..
O and 4th way the best way. find a Uprev dealer Tuner in your area and get it uprev dyno tuned. This way if you have uprev tuner and licence you only pay for tuning and dyno time. if you dont have uprev licence you will have to pay the tuner for a licence which will cost more.
You are able to program your ECU with 5 different tunes and switch it on a fly threw your cruse control buttons while the vehicle is running.
for example.
1 for regular unleaded - fuel economy.
1 for super unleaded - performance.
1 for lets say max. 2 miles per hour speed limit - anti theft.
1 for when you let your kids drive it or someone else maybe 55mph max
1 for towing.

Uprev is better then bullydog. superchips and all other generic programers which used someone's vehicle to make the tune. so you are using generic tune. Uprev is custom tuned for your vehicle.

And I believe Uprev is the only tuner that will allow you to raise the speed limiter.

Had been waiting for my extended warranty to expire before making significant modifications that would risk voiding the warranty.

On the radar are the following:

-Doug Thorley long-throw headers
-UpRev tuner
-exhaust cut out (still want factory quiet at times)
-Supercharger

The first two are no-brainers. Can anyone speak to personal experience with the supercharger or know someone who bolted it on?

Well ain't this tricky. Looks like if I do this mod I will be going it alone.