It's impossible that the sheet should have worked OK in Mathcad 15!
I suspect the unit mismatches are due to an incorrect implementation of the labels used in Prime during the worksheet conversion. For example, if you look at the last line of the Morphologic Time Loop program some of the variables have units removed by the normal division operator, and some by the inline division operator. When the inline division operator is used the units are not labeled as units. I didn't look through the entire worksheet (way too long!) but I wonder if there are not similar problems higher up the sheet.
As an aside, Prime allows vectors with mixed units, so the step of removing the units from all the return values could be dispensed with. It's probably better to get it working first with the minimum of changes though, and then go back and modify it to take advantage of one of the benefits Prime does have over MC15.
