Have you checked the engine and transmission mounts?

 

Was this truck used for towing, or abusive off roading.
With a manual transmission DXing this problem should be straight forward. It started after you replaced the Clutch. I assume you changed out the pressure plate and the throw out bearing too. You should never just replace just a clutch,or just a pressure plate. This is standard for such a job. If you have a defective pressure plate it can cause the trouble you are reporting,and except for the fact you are hearing strange sounds from the back I would suspect a bad pressure plate. I am assuming there is no issues in the transfer case. You have eliminated the drive shafts from consideration, you did check to make sure it was assembled in phase and none of the balancing tabs, if any, had not been scraped off, right . What is left is the rear differential. First question; A bad rear end usually makes a howling noise when there are problems, not always but this is one of the things you listen for. I asked about towing, if your truck was used in such away with a history of overloading it will rip the guts right out of a Clutch and to a lesser extent a rear end. In fact if I am looking at a used truck and I see a well used towing hitch that puts me on guard before I would consider purchasing it especially with an automatic transmission.

I believe your truck has a DANA 44 (9 inch?) rear end. Caulk up the front wheels Put the rear end up on stands and place the transmission in neutral put down a pan to catch the gear oil, more about this later. Pop the cover off the differential referring to the illustration below. Inspect for any damage in the ring gear assembly, chipped teeth gear alignment issues, this is not obvious but a close inspection will show if ring and pinion are meshing properly, this is a very rare problem. There should be a large ring gear on the left side of the differential this is the sensor ring for your rear anti lock brakes. Rotate the differential and see if you can detect bad bearings, a bad pinon shaft bearing, the larger inner, one can cause of the some trouble you are having. Now take a good magnet. I use the ones you can salvage from defunct computer hard drives they are very powerful. If you don't have an old HD kicking around ask around at a computer service shops explain what you want them for and they should just give them to you. I clamp them into a vise-grip and dredge the magnet through the gear oil. There will always be metal shavings what you are looking for is chunks of metal flakes are usually ok, unless they are large amount of them but any chunks of metal are a concern. If there is no obvious problems with the rear end, which is what expect, leaves you with one thing you have a bad pressure plate, which I honestly think is the problem here. I have had cars and trucks with bad pressure plates and it is like driving them into a hurricane force head wind, and if you have bad springs it will cause all kinds of vibration. With the mechanical clutch linkage we used to have you could feel this sort of problem through the clutch pedal, with the hydraulic systems you are isolated from such things. Good luck.

And as TheJMC stated check the motor and Transmission mounts bad ones can cause all kinds of strange sounds.

 

Yes haha we didn't just change the clutch, we got the flywheel re-surfaced, new pressure plate, clutch, and slave cylinder (Thats what had previously went out on the old one) Im not to sure about towing and what not from the previous owner, i bought the truck with 200km on it so its lived a pretty long life. And it being a 4x4 you never know what its been through... Were getting her in the garage tonight and we'll check all these ideas. I really don't want to change the pressure plate again though, that was a bit of a job last time.. oh well, whatever it takes i guess haha. Ill report back to guys after we check it all out. Gotta get back to school!

 

And actually it didn't start when we had changed the clutch, we did that back in the beggining of december, the shaking started about 2 weeks ago max.

 

Oh some other things i forgot to add that might help, I don't think its the pressure plate because when you pop it into neutral it still continues to shake...also when you let off the gas at high speeds it shakes even worse, and when you hit the brake it stops.

 

Not sure this is it but I have a 97, 4.6, 2wd, drum brakes in back. Shaking started last year and even with a complete brake overhaul it didn't go completely away.
Turned out it was the brake flex lines from the fame to the wheel. The internal diameter was closing down due to liner swelling and all the pressure in the wheel cylinder was not bleeding out as it should.
Replaced the lines and no more problems.

Good luck

 

So we figured it!! My dad took the truck to work today and on his way home the shaking just stopped. So when he got back we got looking under there and we checked out the front driveshaft (for the first time) And all the bolts on the front of it were gone! and there were three left on the back but two of them were only finger tight, haha. Also noticed that that one u-joint seemed buggered . So we evened it out and put 2 bolts on each side and gonna pick some more up tomorrow and also lock tight them this time. Also one this weekends we're gonna back the transfer case off and pull the shaft and redue the u's. I think thats kinda how they got messed up, when we did the clutch and pulled both shafts we had to use a propane torch to loosen the bolts up because even the impact gun couldn't get em off!! So i think mighta melted some the seals when we did that and its winter here with over 3ft of snow so waters gonna get in there quite easy. . Thanks everyone for all the help!