rough idle 03 6.0L, couple other ?'s

Just bought the truck in the last month and a half or so and i've put about 6000 miles on the truck. Since picking up the truck heres what i've already done trying to get it up to par before i start upgrading etc.

Truck is a 2003 2500 6.0L 4l80e with 106k on it reg cab long bed 2wd. 3.73's

• New 4l80E from a 26k mile conversion van, full custom valve body/shift kit hybrid between transgo hd2 and my local shops setup.
  
• both knock sensors/ intake gaskets
  
• Crane fire wire 25 ohm wires
  
• AC irid plugs
  
• bilstien shocks in the back not sure about the fronts yet..

This fixed most of the problems and got the truck turned into a pretty solid all around setup.

Now the the idle RPMS stay the same but i feel sharp missfires every once and awhile. Also when i start the truck it revs to 1000-1100 rpms and usually won't drop until after i've had it in gear and drove it. No codes no nothing.. i'm thinking i have a vac leak or something but maybe not.. but the slight miss fire is driving me nuts.

Next i'm leaking out of the pinion on the rear axle.. this is not my strong suit i don't set gears. Whats the normal procedure for replacing this seal.. many problems with the crush sleeve? magic torq number to set the nut etc..

i've got a ton more questions and ideas but lets start with those since i'm new here and i've already wrote a book.

Thanks!
Brock

Di all of these things happen after the work listed above? When you had the new plugs put it, did you gap them properly? Those Crane wires are the 8.5mm, right? Make sure those are seated on the plug and coil pack correctly. You may want to pull the wires off completely and reseat them... And go ahead and get a custom tune... It will solve the rest of the problems...

i gapped the plugs i think they were .40 .50 whatever i found online..or the autozone guy told me, the crane wires at 8.5mm 25ohm/ft premade for ls1's.

The old plugs were original and so were the wires, plug gap was like 80ths from it being melted away so when i got the new wires and plugs on it started running better.. it would missfire to the point it would change the rpms sometimes. But i think the sharp missfires cam in after knock sensors.. but i've checked the intake pretty close.

What should the intake bolts be torqued to?

I was considering doing tbichips.com tune, who got my s10 running on stock TBI setup using v8 injectors on vortec heads, cam, 6lbs of boost and meth injection.. So i somewhat trust him and he works cheap. Said he would completly take off TQ MGT.. is that smart?

thanks again,