'03 Prerunner Suspension replacement and lurching/clunking

Hey all,
I've got a 2.7L '03 Prerunner Extended Cab with 60K on the clock. I absolutely love the truck, but am having some annoying issues which I am currently attributing to possibly worn out stock suspension / axle wrap.

1) Sometimes when accelerating or coming to a stop, I get a "clunk" as the truck knocks forward a bit. The Auto shifter stick clunks around as well when this happens.

From everything I have read on here about axle wrap, I'm thinking this is to blame for this problem. I have yet to stick a camera under there and go for a drive though, in order to verify.

2) my truck seems to surge and buck around a lot when braking. You can be in reverse or drive, no throttle, moving normally at idle speeds, and lightly depress the brake to come to a stop and my head will almost hit the windshield. Good brakes, right? But obviously something else is going on here. I'm thinking the struts and springs need to be replaced. 1st gear also seems to engage rather roughly, and since I'm getting a lot of torque there, I'm thinking it's just pulling the chassis around on my sloppy suspension.

Weird thing is though, the truck doesn't seem to behave erratically when you're actually moving at speed. Nothing feels blown, it doesn't feel like I'm bouncing around too much when I'm actually driving, etc. I really don't know though, this is my first truck. What do you guys think?

TIA
-Jamie

 

Could have something to do with the Tranny mounts/Engine mounts mabye??

 

All mounts and bushings have been checked and are solid. I'm leaning towards replacing the suspension right now. I just can't think of there being another cause.

OME or Nitro front shocks, retain factory coils. 5100 rears and Wheelers 4pack HD leafs.

Hopefully that will do it...