The recommended way to upgrade your file (and retain your notes) from PAF 2 to PAF 5 is as follows:
First: Make sure you have a current backup of your PAF 2 database.
Second: Scan your file for problems and fix them if possible in PAF 2. (In the Utilities Menu there is a "Fix data files" option - use it.)
Third: Open your PAF 2 data file (Indiv2.dat) in PAF 188.8.131.52 (This is available for free download at http://www.familysearch.orghttp://www.familysearch.org under "Order/Download Products"; and is also available on the PAF 5.0 and PAF 5.2 CDs) This will convert the PAF 2 file into PAF 3/4 format, and give you a lot of conversion options.
Fourth: Open the resulting PAF 4 file in PAF 5, which will convert it to PAF 5 format.
Of course, you could always just export your PAF 2 file as a GEDCOM and import that into PAF 5, bypassing the PAF 4 program altogether - but I have had the best results with the steps above.
If you have further questions, you can contact PAF Support at: Help@ProductSupport.FamilySearch.org