Shower stall glass door re-install problem

Shower pan failed - tore out the old pan and about half of the tile (about three feet up on each wall) - new tile and pan installed by a contractor - I'm reinstalling the old shower door, and it looks like the width of the shower sill (where the bottom runner of the shower door goes) is about 1/2 inch wider than where the top rail of the shower door goes. Not sure if it was like this previously, or if the hardiboard the tile guy used on the repair would be different from the original crap put in when the house was built 20+ years ago.
1 - if I just center the bottom rail on the sill, will some extra caulking at each end of the bottom rail take care of the width problem and prevent leaks?
2 - I'm assuming that the vertical rails need to be true (straight up and down) so the door hangs correctly - since the walls aren't square, could I just shim the vertical rails slightly at the bottom to make sure they're lined up correctly - guess I'd have to use some additional caulk there, too?
Using a bar of soap standing out in the rain is looking pretty good right now!
Thanks!
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I believe that caulking will work. My base was not exactly level and the gap between the glass shower walls and the base went from zero to about a 1/2 in. I filled it in with a good silicone caulking and in almost 2 yrs. haven't had any leaks. MLD
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Using Caulk to fill 1/2" gap seems like it be a bit too big .
Not sure if I am visualizing your situation correctly though.
The contractor could have adjusted things to make sure the door would fit. Did he know what you were planning to do?
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It'd be more like 1/4 inch on each side of the base - I didn't specifically tell the guy that did the tile that we were going to put in a shower door, but he had to know - there's now way a shower curtain would work in this situation - and the holes were there (in the tile that wasn't replaced) from when we took down the door before starting to bust up the floor.

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1/4" In that case why not. Make sure the door is rigidly mounted first and use masking tape to get a good straight line
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