Joel,
The first thing I would do is take some time to look over VERY closely what your Lexus extended warranty contract covers compared to what the tech has mentioned as to what needs work should answer some of the questions. I think things such as the water pump should be covered IF (big IF) the unit is failing. Tranny pan gasket & rocker cover gasket, bushings should be covered. Steering wheel shaft boot sounds like it needs lubrication. Car pulling to one side I doubt as that's an alignment issue, unless they find a suspension defect.....do you have the 'regular' suspension or the optional AVS suspension set up? (I have the AVS personally).
What I would do is go to a Lexus dealer of your choice (I have only delt with Lexus of Richmond hill for warranty items personally & they were good.......I have my own independent mechanics who do routine maintenance & service because the dealers in my opinion are way too expensive!) & talk with the service manager directly & ask him or her to put their BEST tech to work on the car, but make sure you know EXACTLY what is & is not covered when doing so. They can at least fix the stuff that is covered by the warranty & give you a quote of the other stuff should they in fact find anything else & make that clear.
P.S. Where did you take the car specifically & what mechanic worked on the car? I too have the extended coverage & it expires in Jan of 2006......I am thinking of taking the car in soon to before my coverage expires. I'd appreciate the info! Hope this helps. B)