For this kind of thing I immediately turn to Excel. 9 times out of 10 if you can do it in Excel you can do it in InfoPath/SharePoint.
You may also want to look at SharePoint and calculated columns.
So if I've understood you correctly. This is how I've just done it.
For each NA you minus 1 from the total of possible questions.
I'm not sure how practical my solution is - depends on the number of questions?
I set up a form up with 16 Question fields. Each question field as QuestionX . X being a number.
I then set up a Calculations section with the following fields and formulas (you could hide this from public view)
Total Possible Answers - count(Question1 | Question2 | Question3 | Question4 | Question5 | Question6 | Question7 | Question8 | Question9 | Question10 | Question11 | Question12 | Question13 | Question14 | Question15 | Question16)
Number of Yes - count(Question1[. = "yes"] | Question2[. = "yes"] | Question3[. = "yes"] | Question4[. = "yes"] | Question5[. = "yes"] | Question6[. = "yes"] | Question6[. = "yes"] | Question7[. = "yes"] | Question8[. = "yes"] | Question9[. = "yes"] | Question10[. = "yes"] | Question11[. = "yes"] | Question11[. = "yes"] | Question12[. = "yes"] | Question13[. = "yes"] | Question14[. = "yes"] | Question15[. = "yes"] | Question16[. = "yes"])
Number of No - count(Question1[. = "no"] | Question2[. = "no"] | Question3[. = "no"] | Question4[. = "no"] | Question5[. = "no"] | Question6[. = "no"] | Question6[. = "no"] | Question7[. = "no"] | Question8[. = "no"] | Question9[. = "no"] | Question10[. = "no"] | Question11[. = "no"] | Question11[. = "no"] | Question12[. = "no"] | Question13[. = "no"] | Question14[. = "no"] | Question15[. = "no"] | Question16[. = "no"])
Number of NA - count(Question1[. = "na"] | Question2[. = "na"] | Question3[. = "na"] | Question4[. = "na"] | Question5[. = "na"] | Question6[. = "na"] | Question6[. = "na"] | Question7[. = "na"] | Question8[. = "na"] | Question9[. = "na"] | Question10[. = "na"] | Question11[. = "na"] | Question11[. = "na"] | Question12[. = "na"] | Question13[. = "na"] | Question14[. = "na"] | Question15[. = "na"] | Question16[. = "na"])
Total Possible Answers Minus NA - TotalPossibleAnswers - NumberOfNA (field names)
Percentage To Use - TotalPossibleAnswersMinusNA (fieldname)
Percentage Calculation - NumberofYes / PercentageToUse * 100 (fieldnames)*100
You mention 6.25. I assume you'll be adding this to an amount somewhere. Not sure what it was connected with or to. Again, hit excel and you'll easily be able to work it out. Yes 16*6.25 = 100 but is it now necessary?