Hi, I wrote TWJCalc and thouroughly endorse what others, but especially Feadoggie, have been telling you.
First I have to clarify something - I do not understand the maths involved in the calculation. Or more accurately I do not understand the theory behind the maths in the calculation. I 'borrowed' the algorithm from two places: Flutomat (by Pete Kossel IIRC) and TWCalc (Daniel Bingamon). I think there is a very small error in the Flutomat algorithm, but it is really insignifcant.
I wrote TWJCalc to answer the question 'how are the hole positions and sizes related', and since I am visually oriented I wrote a program to display the holes as the parameters changed. From there it got a bit out of hand...
Now you need to understand that the calculations are not accurate predictors - not like a metre rule, or a shop till where there is a correct answer that pops out. The calculations are more like a model of reality. Within limits the model behaves roughly like reality - it makes statements like: "increasing this hole diameter means it needs to move down the whistle, and that the next hole up gets smaller". It does not make statements like "increasing this hole diameter by one millimetre will move the hole 0.75mm towards the end". It is not that accurate. In order to increase the accuracy there are several places that 'fudge factors' are applied, but these are derived from reality (making whistles that work and measuring them) rather than from theory. There is no guarantee that the fudge factors are meaningful in a different whistle geometry.
Now if you are making a range of whistles with closely related geometries it would seem reasonable to propose that you could fine-tune the fudge factors so that the accuracy of the model increases. I believe Hans Bracker has done a lot of work on this some of which made its way into TWJCalc as HBFlutomat (Hans' fudge factors at the time applied to the flutomat algorithm). Hans' whistles are highly regarded, so maybe this approach worked.
I used TWJCalc to guide me in making a (just one

) whistle (bass A). I found the calculations consistently out - ie each hole was off by approximately the same amount. This consistency indicates that the model has some merit if fine-tuned.
Sorry for the essay - I have added little really to the discussion, except to reassure you maybe that you are striving for an accuracy which I do not believe the whistle calculators will yield. You may be interested to try some of the different algorithms available, or even use the scripting calculator to fine tune your fudge factors (things like 'end correction').
HTH