New Door Doesn't Open Properly

I bought a new door (pre-hung), and not wanting to pay the $300+ for installation, installed it myself. I wanted to replace the piece of wood the original door had rested on, but wasn't able to find wood 1-1/4 inch thick. I decided just to reuse the existing one. Reinstalled the wood, set the door in, and the RO was too small. Grumbling, I put together some plywood and wafter board and installed the door in partway. The sweep on the bottom of the door was too low and drug on the carpet. Not being able to resolve this issue w/o major work, we finished shimming the door and sealed it. We are going to create a small "landing" area of laminate flooring to remove the carpet, but there is another issue. The sweep, when it is closed, ends up looking like this on the sill /// (looking down the door towards the hinges, and when we attempt to open it <-- this way, it catches, making it nearly impossible to open easily. Is there a way to fix this? The adjustable sill is all the way down. Is there a way to remove this?
Another question I have involves a storm door installed on the outside of the door. In all of the measurements I have taken, it looks like the handles on the storm door will interfere with the handles on the normal door. Does anyone know anything about this?
Whew, a long post. Thanks in advance for any help.
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