I did not get your attachments; make sure to zip them and attach the zip file. Our forum software removes some file extensions automatically to mitigate spamming.
The differences in search output is because words in a PDF document are not necessarily connected logically, the way they might be in a text file or Word document, so search engines also look at the placement of letters to decide which sets of letters make up "words". Since everybody (Adobe, us, other competitors) does this differently, results of searching will differ between products.
There are two ways to help with this. The first is to use the best OCR layout engine possible - the layout engine is the part that figures out how words, sentences, and paragraphs are connected on the page. We have added a greatly improved layout analyzer to our newest offering (the PDF-XChange Editor), and I have tried your document here and the results are a lot better. The second is to make sure documents are de-skewed (ie, level). Looks like your example document is good, but we also offer the Auto-Deskew option in the PDF-X Editor. Both of these things will improve layout, and placement of text into continuous words, and therefore searchability across products.
As for version numbers, for OCR it is really not too critical which PDF version number you create when scanning. PDF 1.4 or 1.5 are fine choices. I wouldn't recommend using PDF/A-1 and PDF/A-2, since these are restricted formats (the "A" stands for "Archiving", so a lot of operations are not allowed on these files in an effort to preserve the integrity of their contents). PDF/X also has some restrictions on it.