First follow the good advice found in the posts above.

Beyond that, my questions are:

1. What was the very last thing done to the bike before the problem started (i.e. FD shifter and/or FD cable replacement, rear wheel/ hub/gear-set change, etc)?
You mentioned that the "a shop said it might be due to the crankset not being lined up correctly because of being taken apart and put back together. This has only been done at most 2-3 times to replace the bottom bracket." I would, as others have mentioned, start with the crankset and bottom bracket. I'd carefully check the newest bottom bracket length against the original BB (if possible). However, I think the "2nd shop" and FBinNY are correct in saying that the problem is due to "taking the crankset apart" and then re-assembling it incorrectly. This could very well be your problem.

2. Did the bike suffer any damage before the problem started (i.e. crash or moving damage, slightly bent rear triangle, etc)?

3. Did you yourself measure the chain line and, if so, is this measurement with specifications? Note: measuring the chain line "from the riders perspective" does not always mean that it's within specs. Also keep in mind that some crankset/bottom bracket and/or FD combinations can be "incompatible" in regard to proper chainline and/or shifting.

4. Is the FD shifter and cable in good condition? And is the cable of the proper size/type and correctly routed?

I too would suspect an improperly assembled crankset (if all else checks out OK). This, of course, means that you'll need to either correctly re-assemble the crankset (as mentioned by FBinNY, etc) or replace the crankset (as mentioned by the "2nd" shop.