You can either go to the towers a day or two before you want to go to the top, or there's a privately operated website (not associated with the PT) that can help you (don't recall which one, but seem to recall it's been discussed on FT... try a search?). We didn't get to the towers as it didn't fit properly into our itinerary (closed the only day we could go).

If you haven't considered the Hilton in KL you might want to check it out. It's by no means your typical Hilton property--they could probably re-brand it a Conrad if they wanted. Get an executive level room--the lounge is one of the best in the system--it's probably one of the better hotel values around.

As mentioned in the other thread (flooding), it's probably too soon to say whether the worst is over for BKK... guessing it'll be another 10 days before we know how it plays out, but T.I.T., so who really knows?;)

Bangkok
Take the airport link instead of a taxi to the skytrain and stay at the Sheraton Grande Sukhumvit, with it's own skytrain station. Should be able to get around fine above ground.

Re: KL...
The Traders has that great rooftop skybar/pool.

Being an SPG person, I loved the Westin for location. Nice mall across the street. Had a great Petronas Towers view from my room but YMMV. It's usually available on cash and points.

We just woke up early, walked to the towers in the dark and stood in line for a ticket. Last tour of the day gives you daylight and dusk time up there.