Yes, you change the CRiP (CRank Index Position), (in your example, by adding or subtracting 5) to get the timing to agree. You can change this number right on that Adjust screen and see the effect.
I doubt the base fuel map is using the MAF (well maybe the air temp part of it). Most MoTeC setups use either MAP or TPS for the load axis.
A base fuel map is just something to get started with -- you will need to tune the fuel and ignition tables to give the engine what it needs. Preferably this is done on a dyno, but can be tuned on the track (or street) if you are careful.
If you are going to tune this yourself, you might be interested in some of the courses over at HP Academy. They have some intro webinars that I think you can see for free:
https://www.hpacademy.com/