Did the same experience with FS Repaint. I even took all textures ( bump, LM, spec) and copied them into the aircraft's root directory avoiding any fallbacks. It still took 3.5 minutes. But no blank spots anymore.
I abandoned FS Repaint and usualy load the plane directly in FSX. If not OK I pause, minimize FSX. Return to the paint, correct and load the texture. Then back to FSX I simply reload the aircraft and the livery updates. I admit you need a tough PCU  ;). Latest at 2 o'clock in the morning all cooling fans run at high speed. :-?
I also agree with Dave that it is not possible to build one giant texture including upper and lower fuselage in one. So far I combined textures 4, 5 & 6 for the lower fuselage as well as 7,8 & 9 for the upper fuselage. As the textures overlap I recommend you use panelfinder (freeware, just google.) and maybe panelfinder-extension. Make an aircraft with all textures made from panelfinder bmp and fly. Take a lot pictures especially at spots you have problems. Put a copy of PF in your texture files and acc to the pictures taken you can adjust / join your textures. Same for the tail. Very nice to see where the rudder fits in your texture (stretch, rotate...)  :'(
For the center layer on top of the fuselage you have to play with the coloring. f.expl if your fuselage is white, take a white like 220 220 208. for the center part only try 233 233 226. Just give it a trial and see if that's working out for you.
nice weekend
Lex