Ok,here is the truck
2008 Ram 3500 4x4 Megacab Cummins 6 speed Auto.
74,000 miles - Previous owner used it to pull a 5th wheel 90% of the time.
Mods are:
1.DPF delete
2.EGR delete
3.EGR Cooler delete
4.AFE intake
5.H&S tuner - Set at MILD tune (stock,mild,wild,hot)
6.5 inch turbo down/short turbo style muffler that splits into dual stack out the bed.

To explain: I bought the truck stock and did the modifications myself,Prior to the mods I had no issue's with the truck.Since the mods I have only put about 6,000 miles on it.
I noticed the vibration almost right away after installing the dual 8 inch stacks in the bed,So at first I just chocked it up to the stacks vibrating at certain sound waves or driving condition's,It has been getting worse though.
When towing my 34ft bumper pull RV I'm getting a vibration that is quite noticeable when the engine falls to a certain RPM.
To explain this best,I will approach a hill or incline while towing in TOW mode and as soon as the truck starts to labor the vibration will start and get worse until it down shifts. The gear doesn't matter it will do it in 3,4,5 until it down shifts then all vibration stops.
I also tried this: When going down hill I would just give it enough throttle to start pulling or accelerating and it will vibrate until it shifts up reguardless of gear.

It seems to me to be a driveline issue, U-joint's,bearings,transmission?

Any idea's on where to start or is there any "known" issue's?

Thanks for any help!

 

1 Known issue is the 2 piece driveshaft. It is a source of vibration and has a weak carrier bearing. I replaced mine with this:
http://www.doghousediesel.com/catalog/i259.html
and have not had vibration since.