I talked to some people. And well, i guess the indexing can be a factor.
But moreso, with the u-joints on my truck being non greaseables, I cannot rule them out on being bad or rusty inside and causing the vibration by greasing them. So looks like i'ma be replacing them here soon to rule that out. It is most likely my problem.

If it is not, I'll keep moving the driveshaft in 45 degree intervals till it is close, then zero it in.

The driveline angle is not gonna be a big deal i have found out by just being a half inch lower.

So, my best guess is the u-joints right now.

 

Well, from driving the last few days, and having the vibration come and go, i'm pretty sure one of those non greaseable u-joints is at fault.

I should save all the bad non greaseable u-joints and throw them in my aunts neighbors face, he thinks they are the best thing since factory sliced bread.
"They will never go bad, cause they have the right amount of grease"

haha, okay whatever, maybe in a perfect environment.