@MudWaspSR5 I know it's been a year and a half since you asked, but I thought it was still worth a reply since I have a lot of experience with the 1GR-FE manual trans Tundra. There were some head gasket issues on the early 1GR-FE engines, but Toyota had resolved that problem by early 2006. Aside from that, it's a great engine. I've owned two, an 05 Tundra with an automatic and an 06 Tundra with a manual. They have plenty of power (granted, both of my trucks were base model regular cabs, so they were only a touch over 4000 lbs). The 4.0 has essentially the same horsepower rating as the non-vvti 4.7, just not as much low-end torque.
I bought my 6-speed manual Tundra with the intention of doing a 4x4 conversion on it. Toyota only offered 4.0 Tundras with 2wd. I eventually figured out why. After a 3" lift, 34" tires, high clearance steel bumpers and rock sliders, I was ready to tackle the transmission and transfer case. My truck started with the RA60 transmission, the 2wd version of the 6-speed. The two 4x4 transmission options for the swap were the RA60F out of a 2nd gen Tacoma or the RA62F out of an FJ Cruiser. I went with the latter for its overdrive gear ratio of 0.799 (compared to 0.85 in the RA60F). This translates to running maybe 200 rpm less at highway speeds. As far as I know, the two transmissions are the same aside from the 6th gear ratio. There is a known issue with these transmissions where the clutch release bearing rides on a part of the transmission that is aluminum, digs in eventually and causes squealing noises. Toyota made some changes to address this problem, but the best solution is made by URD, with a stainless steel sleeve for the bearing to ride on and a different bearing that fits over the sleeve. I opted to add this upgrade while I was in there. Of course, the transmission mount didn't line up after the swap, so I had to buy a MIG welder and learn how to use it before the truck would run again. The center section of the transmission crossmember had to move down about an inch and forward about two inches.
Next up is the transfer case. The 6-speed manuals have an output shaft that is different from all of Toyota's other transmissions. It is bigger in diameter and has 22 splines (where everything else is either 21 or 23 splines) That means there are only two bolt-on options for the transfer case. All of the manual transmission FJ Cruisers had full time AWD cases (with a locking center diff) and the Tacoma 6-speeds all had transfer cases that were electronically shifted. Neither of those was what I wanted. I ended up buying a J-shift case from an auto trans FJ Cruiser and a t-case from a manual trans 2nd gen Tacoma, then I swapped the planetary and input shaft from the Tacoma case onto the FJ case. That gave me a J-shift case that would bolt on to my RA62F transmission.
Next up was re-gearing the rear diff to 4.56 and adding an Eaton TrueTrac. After that I upgraded the battery and added a winch. The truck is quite capable off-road at this point, but still 2wd.
The attachment points for the front diff are present on my frame, so I figured the rest would bolt on. I was wrong, the diff didn't clear the oil pan, not even close. Then someone pointed out that my engine had a 2wd oil pan. So I bought the 4x4 oil pans (upper and lower) for the 1GR-FE. I ended up having to cut out a big chunk (and weld in a reinforcement plate) of the crossmember that the steering rack is bolted to for the new oil pan to fit in. I did gain some oil capacity and have a much deeper sump, but the front diff still doesn't fit.
After some more research, I finally figured out that the layout of the Tundra frames requires a front sump oil pan for the front diff to fit where it is meant to sit. The 3.4 V6 and the 4.7 V8 both have front sump oil pans, but Toyota never made a front sump pan for the 4.0 V6. If you look at a 2nd gen Tacoma or an FJ Cruiser, they have the steering rack mounted to the front of the front crossmember, then the front diff behind that crossmember, followed by the rear sump oil pan then the 2nd crossmember. On the 4x4 1st gen Tundras, the front crossmember is followed by the front sump oil pan, then the front diff, then the 2nd crossmember which has the steering rack mounted behind it.
I've come to the conclusion that the only way to finish my 4x4 conversion is with a Solid Front Axle. I'll get there eventually, but it's going to take a while.