I'm doing a MARPAT Camo Pattern with Duracoat.  The instructions say to complete apply all colors for a multi-color job within a week.  The instructions didn't explain why, NOR did they give any alternatives if you pass a week in time between start to finish.  I can only assume they intent is the coat cures enough within a week that additional top coats are NOT recommended.

Well, I have drastically underestimated how time consuming making the patterns for good MARPAT job is, and I got 3 colors down in a week, but I'm past 2 weeks and just finishing applying all the patterns for the last color.

Should I just spray and hope for the best?  I should I try to sand or sand blast to rough up the surface some?  Any other suggestions, or knowledge of what my options or possible results will be?

I would lightly sand before you apply the next coat.

The paint won't cure in one week, usually 3-4 weeks. The paint my be dry, but still needs to release solvents. Here is the reason why DuraCoat wants all the colors applied in one week...they want the layers of paint to fuse into one layer.  You get outside of the one week window, you are going to have something more like layers of paint over layers of paint. The top layers of paint won't be fused to the lower layers, so it will stratch off from the lower layers easier than if it was multipul layers fused together.

Yes, you can go back later and scuff the surface with a red 3M scotchbrite pad. But here is the main draw back, it's going to be hard to scruff it properly without ruining your masking job. You need to scuff all the shine off the paint, esp important near the edge of your masking material. Scuff your surface with light pressure, let the scotchbrite pad do the work. If you scuff with a lot of pressure you will just put deep scratches in the surface. Two things will happen if you do a bad scuff job; you will ruin your crisp masking line and the egde of your design will get fuzzy, if you don't scuff good enough then edge of your painted design will chip off easily.