I'm about to change the water pump and timing belt on my 2000 LS400. My biggest question is how to make sure the timing is set correctly before AND after removing the timing belt itself. So far, this is what I'm understanding, jump in when you see something wrong:

1) Before any disassembly, set to TDC. Crank pulley should be at "0" and the two notches on the camshaft gears/pulleys should be at the TDC mark, the "I" line. (NOT lined up with the "T")
2) Just before taking the timing belt off, rotate the crankshaft so that the camshaft pulleys are 50 degrees PAST Top Dead Center -- meaning the cam pulleys should now be lined up with the "T". I understand the "T" marking is specifically for taking the belt off, and that this step is to avoid unwanted camshaft rotation...?
3) After setting to 50 Past TDC, undo the t.b. tensioner and slide the belt off.
This is where I get confused:
4)With the new belt slipped on, put the crankshaft to TDC? Forgive me but, shouldn't the new belt be placed with its markings matched up to exactly what markings were on the old belt? I have feeling it doesn't work like that. From here onward, I am stumped as to what the crank AND cam pulleys need to be set to.

I've been all over different forums, write-ups, and Youtube videos and I cannot find a straight answer. It's rare that I ask questions on forums, so as you can tell I'm really stumped here

 

Please see the attached PDF's from the service manual, if they don't download in order please note the sequence numbers.
The answer to your question is found at EM-25 No. 18 (c)

 

I wish those PDF's were found more easily. Thank you, I'll look those over tomorrow.

 

The TB service isn't for everyone but it's very doable if you're competent with the right tools and you know your way around the engine compartment.
You're obviously planning ahead, which is smart, but I can't stress enough the importance of staying organized! It's very time consuming and the fasteners will pile up if you don't keep track of them.
I've found putting each fastener (bolt nut screw whatever) back where it belongs after removing a part is the easiest way to keep them in order. Just screw it in a few mm, enough to hold it in place, until you come back to it. This way there's no confusion especially with the water pump bolts as it alone uses 8 or 10 IIRC most of varying lengths.

 

How did your timing belt job went?
I did my 99 TM, water pump, tensioner camshaft seals and everything else that can be replaced here.
After putting everything back together I have a horrible tapping noise from the valves, the car runs great, but the noise is almost like a diesel engine on idle.
I didn't mess with the Valve shims, and there was no noise before I worked on the car.
I can't figure out what is causing the tapping noise, I was wondering if anyone has had this issue

Thanks