Glass shower door caulk selection

I've just finished removing all the glass and metal hardware that was the door to my fiberglass shower stall. Silicone caulk was used on the door frame sides and there was a bead on each side of the threshold. But under the threshold was some white, flexible caulk that acted like it never really cured and there was a lot of it.
I'm doing my best to clean everything up and hope to hit a boating supply store this weekend to see what kinds of caulk remover they sell.
What I'm not sure of is what the under-the-threshold caulk was. I know if it had been silicone I may not have been able to get it loose, so I'm interested in using similar stuff again. Does anyone know what this stuff is and what I need to buy?
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The material may have been a mastic. The wrong material for the job because it doesn't cure.
Silicone caulks have become the favored caulk but in my opinion silicones are the worst material that can be used. Silicones (siloxanes) typically are molecules that are difficult or impossible to attach to once cured. Consequently, when (not if) the caulk fails or leaks it is not possible to repair the leak since additional silicone caulk won't attach well to the previously cured silicone.
I prefer to use a urethane caulk. It is messier to apply, but far more durable and repairable. I mask the sides of the caulk bead and remove the masking tape when the urethane is partially cured.
Bostick is a good supplier as is 3M. 3M's urethane caulk will be found at any good boating store. I've bought it at West Marine.
Boden
Abe wrote:

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