My 1999 Toyota Avalon is running rough and vibrating especially when put into gear.

If you have 2 cylinders that have absolutely 0 compression, to state the obvious, that is a serious problem, stuck valves or something. If the timing belt broke it would not run at all. I need to go look and see if it is DOHC, one cam is not turning maybe

Yeah, it's a 3.0L V6 DOHC, one cam opens exhaust the other intake, as opposed to one cam opening valves on one bank. I don't know the lay out, which is 1 and 2 on the same side? Or 1 and 2 on opposite banks.? With proper maintenance that engine should go well beyond 131,000 ..my point being one cam could have the sprocket stripped or broken off cam, not turning, and since it operates valves on 1 and 2 both be it intake or exhaust, there is your no compression. You may not need a NEW motor but the top end is going to have to be looked at.

This is a lot of work. Please pay close attention to the last two sentences. Disconnect any component needed to access the timing belt covers. Remove the mounting bolts on the lower timing belt cover with a socket wrench and disconnect the lower cover. Release the clamp for the engine wire protector on the rear timing belt cover and detach the engine protector. Remove the mounting bolts for the upper timing belt cover and disconnect the upper cover. Disconnect the bolts for the right engine mounting bracket with a socket wrench and remove the bracket. Disconnect the the guide for the timing belt. Turn the crankshaft clockwise to align the timing marks for the timing belt. The groove on the crankshaft pulley must align with the mark on the oil pump. The timing marks on the camshaft pulleys must align with their respective marks on the rear timing belt cover. Remove the bolt for the crankshaft pulley with a socket wrench. Loosen the two bolts for the timing belt tensioner alternately to keep the timing belt aligned. Disconnect the timing belt tensioner and its dust protector. Detach the timing belt from the pulleys. Try to turn the camshaft pulleys by hand. If one freewheels, the pulley is broken off of the cam. It should turn, but not without some effort as it is opening/closing 12 valves. This advice is a lot of work, please don't even begin if you don't have the time or tools and is not a guaranteed thing, only to see if my suspicion that one camshaft is not turning is correct. I could be way off the mark but with 0 compression in 2 cylinders it's my best shot.

Afterthought: it will run on one bank. That is what led me to my conclusion. There are other possibilities, it has good compression on the other 4 leads me AWAY from the sprocket and entire camshaft. A cam can break. Rare but happens. geez it would be wise to wait and see if anybody else has a better idea, if nobody else chimes in, well, redundant but it's my best shot..and if you bought it from a dealer report his ass to BBB, if just some guy from the listings, he knew he sold you a POS , and you have to do SOMETHING to see what's wrong

Good compression in the other 4 renders this advice useless. I'm having second thoughts...but a camshaft can break, rare, but happens. But I suppose you have to so SOMETHING to figure out why there is 0 compression in 1 and 2. By looking at both sides with the timing cover off. START WITH JUST valve covers off before you really rip it apart look for differences, anomalies from one side to the other. I simply can't come up with anything but valves for 0 compression and you may want to wait until somebody else has a better answer. I don't want to send you off tearing it apart on my account and be way wrong

IT HAS A VALVE PROBLEM THERE ARE 4 VALVES PER CYLINDER ALL IT TAKES IS 1 OF THEM NOT SEATING CORRECTLY IN THE VALVE SEAT AND LEAKING THE COMPRESSION OUT BENT VALVE? burnt valve? a cylinder leak down tester would tell you whats up ///// WGS