When first started on rare occasions it will studder and need a little peddle, but idles fine after that. That hasn't happened yet with this issue. When I first start it it idles at 7200 (around 8 is proper if i remember) and when put in gear it drops to 6500. When idling and rolling without my foot on the brake it idles a bit higher, but at a stop in D with it in gear it idles at 6500.

im assuming you mean 650rpms? that is about 200rpms to low. adjust that 10mm nut up and see what that does.

Ok so I was off about the idle because there are only 3 slots between 5 to 1 which means 1k should be 9. That's confusing. It's still idling lower than it was though.

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Ok, so i was able to take it out on the highway and really romp on it. Still reaches 35psi. It just doesn't "catch" like it used to, engine winds up going up hills but the torque just isn't there. Really feels like the torque converter, but that wouldnt explain the idle drop. Also I went from Lubbock Texas to Denver, that's an altitude change, would that have anything to do with it posibbly?

a boost leak WILL affect the idle quality, i had about a 2 inch split in mine and wasnt was sucking hard causing my truck to idle at about 400 rpm i put duct tape on it when i found out what i was to get it home it idled right back up, but you shouldnt have a boost leak if you making 35 pounds.

On another Note. The engine does vibrate a little bit in neutral at 1000-1050rpm. And this disappears at 1100-1150. Egts are substantially higher cruising.

Have the timing checked. It is likely to slip with the 4k gov springs.
torque the nut after it is reset to 140-150 lbs.

or to 250lbs

Do you mean the idle nut or 4ksgk

I am referring to the injection pump nut on a p7100 motor. It takes a lot more power to turn it to 4,000 and the stock torque number is too low. This is IF the timing slipped, or needs reset. By the way have them set it to 15-16 BTDC.
Better MPG and power.