The 4.0 Swap Done!
So I must say that this swap was totally worth it!
However, at times it seemed like a very tall expensive mountain.
Story on initial start up and run. (If you have already done a 4.0 swap, some of this may seem similar to your experience and you may not care to read this.)
So I made it home for the first week of spring break and I was stoked and excited to get that engine in my truck as fast as I could. All the wiring was done so all I needed to do was throw that engine in and start her up... or so I thought. Connecting the gas lines was a piece of cake and I didn't need to change anything for that. The exhaust also went on without any problems and the engine mounts for the 2.9 didn't need to be changed. Now the complications. When I finally had the engine in and mounted to the tranny, I began to connect all my electrical and install the radiator and the fan. I quickly noticed that some quick fabrication needed to be done in order to keep the 2.9 throttle cables. So a custom bracket was made to mount these cables to the manifold because the 4.0 had a different mounting bracket then the 2.9. (I can post a picture of this bracket if someone asks me to) After this, I began to install all the random things in the engine compartment like the intake and radiator and vacuum lines and power searing pump lines and so on... When I was installing the radiator I noticed that there was no clearance between the electric fan and the engine so I had to reverse the wiring on the fan to make it a pusher and mount it to the front of the radiator. With this I had to do a little trim job of some of the sheet metal in order to make it fit just right. (again I can post pictures of this radiator/fan set up if someone asks) By now everything was plugged in/hooked up and she was ready for some fluids and the initial start up. While filling the radiator it began to leak like a sieve. So i ran to the store and picked up a new radiator and filled it up and attempted to start it up for the first time. I turned the key and all she did was crank... no start... some quick trouble shooting figured out that I had no spark so I checked the ignition module and crankshaft position sensor for voltages and resistances. I had a bad Crank position sensor. I put a different one on that i had sitting around and then when to start her up...She fired up!! However... there was a really nasty grinding sound... the starter was shot and was not disengaging. So I ran to the store for a starter and then fired the engine up again. It was running but the throttle response had like a 2 second delay... installed a new TPS and the throttle response was fixed. Now it was time for the first test drive down the road. A quarter mile down the road my radiator cap popped up and shot anti freeze all over the windshield...(the hood had not yet been installed) I found that the cap was bad and was not sealing. To the store again! lol After the new cap I started her up again hoping not to run into any more problems (I had purchased the original radiator and starter from the same guy off Craigslist... needless to say I got ripped off and I will likely never buy mechanical crap from anyone on Craigslist again)...On the start I sat there listing and everything seemed to be running well except for a high idle around 1500 rpm

Noticing that my temp gauge and oil pressure gauge were both not working I changed those sensors out with the sensors from my old 2.9 because they were the same. After that all my gauges worked properly. Anyways, after a few days of driving around town I was able to relax and see that I was in the green zone. It was a success!!
The power difference was amazing! With my 2.9 I always had to drop her down to 3rd gear while climbing the 6% grades on I5, Now I can climb them in 5th gear! I would say that is enough right there to prove the power difference.
Lastly, here is the page I used to figure out which pins I needed to re-pin in the main engine bay plug. Those 7 pins where the only part of the re-wiring process that actually required two seconds of thought. There were two plugs that had to be rewired on the driver side fender but they were color coded so it was easy as pie!
I am sorry this was so long but I just thought I would let everyone know about some of the issues you may face while doing a 4.0 swap.
I will post any pics that someone may need if it will help them.
Thanks to everyone that helped me out and who answered some questions.
I can now change my engine size below my avatar!!