I have both books and I rather prefer the Modern Arms Guide as is. Personally, I think you would be better off tweaking d20 Modern to more closely follow Spycraft than the other way around.
The Spycraft concept of rolling different action dice depending on your level and using them to activate criticals or threats is a great idea. I also like the Spycraft autofire rules better than d20 Modern.
Other than the fact that the Soldier class in Spycraft should have a higher Defense score, I consider the games largely interchangeable. Just change hp to vitality, ignore the initiative bonus in Spycraft (or add it to d20 modern classes) and give everyone wound points and they are the same.
If you are adamant about using strictly d20 Modern rules then you can still use all the guns right out of Modern Arms Guide with little to no tweaking. Just ignore any critical range other than 20 and all the error threat numbers for the guns. The damage, range, ammo capacity, all translates perfectly as is.