Alex? I hadn't seen this build until today.
I can't believe someone didn't direct you to www.4BTSWAPS.com. 
It would have saved you countless hours of frustration in finding and sourcing parts and information you needed to complete this repower.
Even Gaducker is over there with a build thread.
It could have, and still will, save you a bunch of frustration because there have been many 4BT swaps into Jeeps done over there. Also it is a good source for parts.
I went thru your build thread and saw some of your trials and tribulations. Virtually all of the questions you had could have been answered easily as they have an archive of hundreds of builds.
To answer some of your questions.
You don't need a waste gated turbo, what you've got will function just fine. Even if you pumped up the HP with a bigger turbo you wouldn't need the waste gate. 105 HP will move that Jeep with authority. 120HP is the highest you can go without an aftercooler. You need the bigger turbo and after cooler to get past 150 hp and above.
At 105 HP the engine has the same torque as a 350 Chev motor. If you get a ride in a mid 90's Dodge 3/4 or 1ton truck with a 6BT in it, you will get an idea of how fast the Jeep will be. Actually the Jeep will be a little faster because it is proportionally lighter than the truck. The 4BT is 105HP and 275 ftlbs of torque and the early 6BT's were 160 hp and 400 ftlb. or 33% more hp and torque with 33% more cylinders. Difference between 4 and 6 works out to 26.66 hp per cylinder in that state of tune.
You will probably twist the rear axles off that AMC rear end quickly so be looking for a Dana 60 or Ford 9" to replace it. You've got the gearing right with the 3.55's. Look for a Dana 44 (IH Scout) for the front, and you'll need Ford hubs if you use a Chev D44 so you can maintain your 5 on 5.5" bolt pattern.
If you must have the larger turbo get one off a 6BT (HY35) and be done with it. You'll have to either make a manifold by cutting the end ports off a 6cyl manifold, or make an adapter plate.
The only other concern I have is with your front steering. I didn't read all the text, but in the pics it appeared that you had the axle rotated back severly to get the steering arms to clear the spring over. This will result in too much caster angle and the thing will steer badly. 4 degrees is the correct amount. The correct spring spacing is 27" CTC, You may have to modify your spring perch to achieve this number.
When I made my Hi Steer arms in 1992 to be used with my spring over conversion to my CJ5 I had to bend the arms upwards, this took a Rosebud torch and a 100 ton hydraulic press. See pic.
Did anyone mention that it would be a good idea to reinforce your frame center section? with the extra weight of the 4BT it will be necessary. There is a guy here called Chief Wahoo who makes a kit that you weld onto your frame. You can always tell a Scrambler that has been used hard as there is a little wrinkle in the body just behind the door. This means the frame is tweaked, Chief's kit will prevent this from happening to your frame.
I will say you started with a nice looking Jeep and when you get the repower done you'll be pretty happy with the result. Guys are getting 31-33 MPG on the highway with the same combination of parts as you have.
If you need any info on using the Cummins motor in a Jeep don't hesitate to ask. I have a build thread here titled "the DeScrambler Project" , and over at 4BTSWAPS.com the entire build is on my thread entitled
"Here's the DeScrambler."
Randy