I have a 1993 Pontiac Bonneville 3800 S1 and its a little loud. Okay 3 things are wrong with it.
1: It has a medium loud knock when I start it up but when it heats up it goes away.
2: If im going 35-45mph and gas it to get to express way speed it studders sometimes , like its really trying to go but exceling really slow.
3: Its a 93 and I havent changed the fuel filter 138000 on the car.

Any facts or ideas? I have a hunch but want others opinions before I jump on in. :?

Deffinately change the fuel filter then. im not sure how many miles a person can before a change but they are cheap and not too hard to replace. im no mechanic but from my experiences, a new filter will do nothing but good for your car.

Well for number one, first try to dettermine where the "knock" is coming from, my guess is the lower end.
Question number two: Check for any driveline codes like TCC solinoid or Shift Solinoids.
Question number three: Change that Fuel filter ASAP!

If the knock goes away when the engine warms up, it'* a good chance that you have a lifter starting to fail. These engines use a hydraulic roller lifter and when they start to fail, the oil cannot pump up the lifter as fast as it used to do. It will be ok for a while, but don't beat on the car. This is only an experienced guess, have a shop look at it, one you can count on.

The stuttering may be from the fuel filter, clogged and not giving the engine the fuel it requests. It could be a host of other thing, but start with the basics. Do a full tune-up (plugs, wires, fuel filter, air filter, pcv), then see where you are at with the hesitation.

Could I pull the lifter out myself and clean it up or is it a hard job on the 3800 to get to the lifter...

It'* not a hard job, just time consuming, especially for your first time doing this kind of work. You'll need to replace the lifter; it can't be cleaned. I would suggest that you replace all of the push rods and lifters at one time...saves the headaches later. The intake manifold come off, as well as the valve covers and a few other things. Either the Chiltons or the Haynes books can give you the complete know-how on this. If you don't have one, get one. It'll help you in the long run.

Yeh I have a book but I have done it before just not on this engine because on alot you can remove the rocker accembly then pull the rods out then you can just life out the lifters.. is that a possibility?

Almost, you've got to remove the upper and lower intake manifolds, as well. That'* the pain. Change your intake gaskets at this time. You'll be better off in the long run.

Why what does the intake manifold do to get in the way?

The lifters are located under the intake manifold. Once the 2 parts are removed, you'll see them right away. The pushrods run high in the heads and the lifters are actually located in the block. They have a retaining bar that holds them in place. Check that for wear - if a lifter is loose, that could be part of the problem.