Okay, caught my breath. I'm happy the warning was unnecessary!
My exercise was based on the premise that the fret placement discrepancies were "errors" relative to equal temperament intonation (call it my hypothesis, if you wish), and the purpose was to determine to what extent these "errors" might be somewhat optimized (as you correctly understood) by moving the nut, and accordingly, the saddle/bridge.
As I said in a previous post, this exercise with its underlying assumption proved very useful with a courting dulcimer as the only significant error after an initial saddle/bridge adjustment was the nut placement. But in the case of my Maxwell and your Tulip, one look at the initial "error" plot shows that the discrepancies are far and away beyond what one would expect from a respected builder. I went on with the exercise and plugged in the data for a nut and bridge correction anyway. While the theoretical correction "averages out" the discrepancies okay (the R-squared value of the regression showing the residual linear trend was now insignificant), the discrepancies remain intolerably large. Put another way, a nut adjustment would adjust the slope of the trend line but essentially do nothing in regard to the error variance about the corresponding trend line. This came as no surprise, plotting a theoretical correction was purely an academic exercise. The initial plot alone made it clear that the corrections required to nut and saddle/bridge would be much too large to be practical and would do far too little to resolve the intonation issues. So the only path to correct equal temperament intonation would be a complete re-fretting job, a path I'm not in the least inclined to take (although I am aware that others have).
At this point, I wondered if I'd have to relegate the Maxwell to being a "wall hanger" aka "DSO" (dulcimer shaped object) or if something else is afoot that could prove my original premise invalid. Enter "Just Intonation". When Ken Hulme essentially said in a post early on in this tread that the intonation of the tulip dulcimer might have been set "by ear", I knew he was referring to just intonation. I had seen other references to it (hard to avoid) but had not read anything that provided enough meat to wrap my head around. Because I was aware that just intonation poses some limitations on play-ability and the fact I had no just intoned instruments (at least not until I acquired those Maxwells, it seems) it was not something that I was inclined to research. In hindsight, I guess I should have been more attuned to the role of just intonation in the history of the mountain dulcimer but my initial interest in the instrument, way back when, was focused mainly on integrating it with contemporary music. After a few years that first dulcimer became a mantle piece mostly, taken out only to dust off, perhaps humidify and (just maybe) strum a little. That changed a couple years ago when I started playing more regularly and then was struck with the dreaded "DAD" (dulcimer acquisition disease). My Maxwells are party to that affliction and my concerns about their intonation coincidentally coincided with Bridge's reported issues with his tulip dulcimer. My initial efforts to seek remedy were based on a false premise - its like I was trying to grade apples with a standard applicable only to oranges.
Right on cue Strumelia suggests I should investigate just intonation (already in my mind) and also provides some useful references - alluding to Robin Clark in the process. Then BAM! In comes Robin Clark with a mini-thesis on just intonation. The fog starts to dissipate, especially after viewing Robin's excellent video "Equal Temperamant v Just Intonation v Meantone on McSpadden dulcimers" ().
Summing up its become clear we're into the realm of human perception versus physics, thus just intonation is something where art meets science. So my future path will be to return my Maxwells to their original state, except for new strings set to an appropriate tuning, then explore noter/drone playing style to see if I can develop greater appreciation for it. Should intonation issues become apparent in that context at least it will be clear that any effort at setup must be carried out with a just intonation "reference standard" in mind.
updated by @jim-hedman: 05/05/18 05:35:35AM