I have been wondering if a completely stock 1999 SLE with a CAI would be able to handle a WOT run or if red lining it could cause damage.Also when launching of the line would it be best to just floor it or give it some time?

In fact, I would encourage it. Not all the time, but it never hurts to give your drivetrain a good work out.

If you are good with upkeep and make sure your car is in good tune, you'll rest easy knowing your car can handle a little loving abuse once is a while

I few full throttle runs are good for the engine, helps clean out some the carbon from time to time.
As for launching, practice. You may be able to put it down, or you may end up spinning the tires too much. Usual rolling into the throttle is best but every car is different.

I dont know about spining the tires. I havnt been able to do it in mine.

Really? There may be something wrong with your car. I have the 3.06 gears but I can roast the hell out of 'em. Even with TC on I can spin(before it kicks in). No, I am not talking about in the rain and snow either, dry conditions. I have to lay off the throttle when I take off during a race or it will just spin.

I've been able to spin the tires (crappy all-seasons) pretty well on wet pavement by using a proper launch technique on my bone stock 99 LeSabre. Have to try it on a dry road sometime this spring.

And the car does seem to run better after a nice full-throttle blast up an on-ramp. There are a few nice ones around me used every other week or so.

Any Series 2/3 should be able to spin the tires at least a little bit without having to power-brake. An */C motor should be at least able to genuinely throw smoke, bone stock. With my current mildly modded set-up, I can break the tires loose pretty much at will anywhere below 25MPH. 30MPH in cold weather.