It turns out the pinion seal i bought from Advanced Auto was a total peice of crap. Stay away from 'Motor City' brand seals. That is what was causing my problem with the preload. The inside diameter of the seal (where the dust shield would sit) was just a hair too short. In turn the dush shield on the pinion flange was dragging along the inside of the seal... thus an extra 25in lbs of resistance or drag on the pinion when i was trying to turn it.
It might have not been a problem in the long run to use the seal, it was just throwing my preload off so it was kind of confusing.
I used BCA National's pinion seal, which is made MUCH better. Infact BCA makes a very quality product, i would recommend them over Timken anyday (for their seals of course). Its not the basic green seal (or orange from timken). Their seals are built MUCH thicker, so it doesnt bend or warp during installation. And their seal also comes with a ring of silicone built into it, something i havent seen ANY other brand do. Very cool.
The whining noise is still there... althought not as apparent as it was before. I changed out the U-joints with no luck. I figured that might have been the problem, although it did fix other issues, i didnt fix the actual one i was going for.
So the issue still remains. The gears make noise.
It is possible that its the Tranny i am using. I have no real way to find out for sure. The transmission was put in mabye 3000 miles before the gears.
But also it is known that if a gear set is set up with a PERFECT heal/toe patern in mind (IE Pinion depth) then it could become noisey. Because a perfect heal/toe patteren is usually impractical. Mainly because differential housings are not all machined the same. I changed the pinion depth with my jump from 3.27 to 4.56. With ford rear-ends, you probably dont even have to. (ford uses THICK gears on all their coorperate rear ends...smart)
Also 4.56 is a BIG gear. BIG gears are known to make noise. This is what randy's ring and pinion told me "if it hasent broke by now [almost 10k miles after install], then you did something right... probably too right."