Ok so this is a better discussion for the digital tuning forum then..
When tuning MS in MAF mode the MAF transfer curve has to be scaled properly first before tuning begins.
You then have two choices for tuning via MAF function, you can tweak the transfer curve at each plot point [requires a very large complex equation that I do have] or you can simply enable a trim table. This table starts out as all 100's and you can manually tune it or even let the auto tune feature do this for you [this is the way I suggest]
Now as for IGN mapping... the MAF and SD tables for IGN are very different and the load values will not fall into the same cell range. My suggestion is to set the tune up so you begin fuel on maf and ign on sd once you have a decent fuel map you can then drive the car and use datalogs to build a maf based ign table.
I actually tuned my M112 build with maf just so I could figure out the best methodology for doing this.