The metallic sound on take off/back up is usually indicative of bad u-joints, even freshly greased worn ones will "tink"
As far as a lot of the sounds go, they were likely there before, its just been 4yrs since you heard them, and now with the "new engine" you are hyper sensitive to all the noises you are hearing.
Can't judge the performance until at least 500 miles have passed, by then the engine should have gone through several heat cycles, breaking everything in, until then as long as it runs smoothly, wouldn't touch it. Also won't be able to judge its true performance until you run 4.56's for the 31's, or slap on a set of 28's.
Yes, could be U-joints, but there was zero tinking when I parked it. If a U-joint goes bad I usually get a mild vibration.
The U-joints in the rear drive shaft are fairly fresh, but since starting this rebuild, I won't be shocked at anything that is unexpected.
I agree that I may be hypersensitive, but I've always been hypersensitive to noises, vibrations, and leaks. Even though its been 4 years, I have a vivid auditory memory of my engine sounds. This is my 3rd truck with a 22, so I'm very familiar with how it sounds when its running like it should.
Whether or not it takes 500 miles to break in a rebuilt 22RE is subjective. I should know more in a few months. I do believe, being around race built engines and high performance engines most of my life, that I can tell if an engine is "feeling" right. The throttle response at this point is not what I expected and I believe there is some tweaking I will need to do, but I expected tweaking.
I certainly can judge its performance without changing tire sizes or gear ratios. I can compare the engine's performance before the rebuild because it will have the same tires and same gear ratio. I may end up with a lower ring & pinion ratio, but that was not my intention when I started this rebuild.
Arguably... Changing gear ratios or tire sizes has nothing to do with the engine's performance. At this point, I am only interested in the engine's performance, NOT the truck's performance with gears and tires. If I built two 22RE engines and tested them on a SuperFlo 902S engine dyno, and one produced 110 HP and one produced 150 HP, which one would make my 5-speed truck perform better if my truck had 31" tires and 4:10 ring & pinion?