Note: not really an answer, but some suggestions.
Sounds to me that Crystal Reports is not following the PDF spec close enough.
I'd make sure CR is fully updated/patched and try genning another file making sure that "tagging" is enabled - tagging defines the layout structure. I don't have a copy of CR handy, but you may have to define a distiller template to use so when you print to PDF you can select that job option.
You can also tell its a bad PDF by using Preflight in Acrobat, it says there is no tag structure and you can do it manually (draw boxes around each item...). Also that there is no language set, and it is somehow compatible with Acrobat 1.3? which isn't supported anymore and should be 4 at the lowest?
Once you have a "good" pdf can export to xml/word and import that to excel. Also, with Acrobat 8+ you can highlight using the select tool, right-click and choose Open As SpreadSheet. You might be able to get away with just highlighting the whole document -- though I'd hope the xml approach would be best.
Able2Extract does some OCRing and tricky fuzzy logic not only to define tags/layout so it is exportable, but also avoids any font, encoding, etc issue - at least to my knowledge.
In the rare case that you can't get a new file, then exporting to plain text/accessible seems to generate a nice flat text file. You could write a vbscript to parse it (adding your delimiter) and import that into excel.