Guys, thanks for all your help. I have since figured out the cause of the problem, and I appologize for not updating this sooner.
In any case, this is how it all started. A couple month ago, I have replaced the fuel filter, as a part of regular maintenance. There are actually two filters, the pump filter and fuel filter, and they are a part of a single assembly that is located inside the fuel tank and accessible though a port underneath the rear seat. The assembly includes the pump, pressure regulator, both filters, suction plate and the fuel gauge sender unit. It all gets removed as one piece, then disassembled so that individual parts can be replaced.
In any case, this problem started a couple weeks after I replaced the said filters. So from all the replies, I have figured that my pump must've died and ordered a new pump. The pump arrived, and I took out the assembly out of the trunk to replace the pump. As I was taking the assembly apart, I noticed that the rubber O-ring between the fuel filter and suction place was torn, and obviously couldnt hold the specified 55psi of fuel pressure. So afterall it wasnt the fuel pump it was a simple rubber ring.
Except it wasnt so simple. I went to the local dealership to get a new ring. However when they pulled their part catalogs, the O-ring is just not there. Theres no part number for it and its not listed anywhere. Another thing is, besides the O-ring theres also a plastic insert/groomet in there that the O-ring gets put on, and that groomet isnt listed anywhere either. Luckily for me the groomet wasnt damaged, just the O-ring.
In any case, the dealer wasnt able to find the O-ring. They checked if it came with any parts of the assembly, such as a new filter or suction plate, and it didnt either. I came back home empty handed. I stopped at a few auto parts stores, but none had anything close to the size.
In any case, I went to Toyota TIS website, and printed out the repair manual for the fuel pump assembly. The repair manual does show the O-ring, and says that it is a non-reusable part, which basically means that it needs to be replaced each time the assembly is taken apart. However the other plastic groomet is not listed even in the repair manual.
In either case, I faxed the page from the repair manual to Darrell at Sewell Lexus, and he too was unable to locate the O-ring. He was able however to locate a different O-ring, the one for the fuel pressure regulator, which is smaller in diameter. In any case, I installed this O-ring for now and my car is able to start and run better than with ripped O-ring, but still way worse than normal.
Darrell suggested to me that the only way to get that O-ring would be to purchase the entire new assembly (thats after I already bought a new pump that I didnt need to replace to begin with). Luckily for me, a friend who works for a Lexus dealership in NJ was able to obtain one of these assemblied and confirmed that it also came.... with no O-ring and no plastic groomet!!! So at least I didnt waste money on a new assembly but I still need a new O-ring!!!
At this point I've located a company that make O-rings, and they had a few in stock that are exactly the size I need, and made from material that is best for gasoline. They are sending me these O-rings, and I will hopefully receive them next week and get my car back to 100%.
This will hopefully be the resolution, but ultimately Lexus needs to act up on this, because clearly this is something that they have completely overlooked, and sooner or later someone will have the same problem. Is there a way to notify Lexus of that? Will they even care if I called the corporate and tried to explain the situation?
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I'm posting the picture of the assembly. This is right out of Toyota TIS repair manual. I've circled the O-ring that cant be located and the O-ring that I'm using temporarily, and I've circled where it says non-reusable part.
As you can see, the O-ring is there, and the plastic groomet is not there.
For comparison, here is the diagram of the parts catalog that Lexus dealers have. As you can see, it shows no O-ring or the plastic groomet at all, so dealers are not able to located these parts.
1) Fuel tank 2) Mount strap Mount strap Back 3) Seat Seat Back
4) Fuel tank Cushion 5) Tank shield 6) Filler pipe
7) Filler pipe Upper support 8) Filler pipe Lower support 9) Filler pipe Protector
10) Pipe shield Outer 11) Pipe shield Inner 12) Pipe shield Ring
13) Fuel cap 14) Fuel cap Gasket 15) Breather tube
16) Breather tube Gasket 17) Cut-off valve 18) Fuel pump
19) Fuel pump Cushion 20) Filter Fuel tank 21) Filter Fuel pump
22) Pressure reg 23) Plate 24) Plate Gasket
25) Tube 26) Sending unit Main 27) Sending unit Sub
28) Connector hose