I should use the epub or mobi source and check it with the original pdf.
The PDF is probably picture format instead of select able text and unless you have some word-scanner that is 100% accurate can you expect reading errors. (sure for older work that is in handwritten form
You need to copy and paste the word to Tooltip Tool and make a commentary module by adding the parameters and the verse numbers with a ÷
The problem is that Greek and Hebrew words that must in Unicode form instead of special front used by the epub or mobi source.
You can download here a commentary module and use Tooltip Tool to "read" the module to understand how it works . (click on "modules' or modulesHD and Commentary then "read commentary file".
You must tooltip the cross-references ( Scripture menu and tooltip OR Crtl+Shift+ T )