I think your theory and approach of incidence adjustment is correct, providing you dont overcompenste by doing both, but the practice of measuring to the bottom of the fuselage on a table may give unpredictable resulst. The bottom of the fuselage may not be parallel to the thrust line. I think an incidence meter to make the bottoms of both parallel would be more in order for this type of redesign. I'm very interested in your results, please keep us posted.

P.S. unrelated tip, I also changed the gear screws with three 1 size larger nylon screws, then ran a clear plastic 90 degree corner molding (the shower type) along the bottom of fuse. This protected the fuse in the event of a hard landing where the gear comes off and protects the fuse from gear impact damage.