Ann, I am afraid that, sadly, I have very little experience with non-homogenized milk, so no pointers from personal experience. But of course, not really knowing never stops me from offering my thoughts ...
My sense is that 1) most people "skim" the cream off the top of the milk, after letting it separate (thus the name "skim milk"), and 2) I don't think you want the milk to be
entirely free of fat - as best I recall, parmas are generally made with milk having 2-2.5% fat content, or something like that. (Better check that before taking my word for it, since I'm going on fuzzy memory ...)
As for the MD088 instead of 089 -- actually they are the same culture blend, just using slightly different strains or subspecies or something like that. The idea is that, in a commercial operation, they will rotate among various strains of a given culture over time to prevent problems that can occur with large-scale use of the same culture all the time. (Not sure exactly what those problems might be ... build up of "resistance" to a given strain??) Thus, Danisco offers MA011, MA012, MA013 ... all the same culture, but slightly different strains. Likewise they offer MD088 and MD089, and MA4001 and MA4002, and so on.
And again, this is a very forgiving cheese, good for experimenting. If you don't have MA011 and/or MD088 and/or TA061, don't hesitate to use other mesophilic blends. For example, MA4001 (or MA4002) would be a good blend to try with this. Flora Danica would work as well, but will acidify much more slowly, so may benefit from longer cheddaring. And there are any number of others ....