I've done this exact project some years back where the rafters were 2x4 and 16 feet long. That roof was sagging in the middle like a Chinese pagoda! 5-6" of deflection in the middle. We ran some string lines to see how straight (or not straight) everything was and used string lines to make all the sistered 2x6 line up in plane. When it was all done and drywalled it was dead flat.
I don't think you'll need much more than the 2x6's sistered to the rafters. If you cut the angle into the ends first you should be able to fit them in there to run pretty close to the full length of the rafters. But in practice, they don't have to go the entire length to strengthen the roof if they're sistered and joined well. If you come up a couple inches short, what's that really going to do? A 2x4 isn't going to deflect over a 2 inch span in this scenario. The rest of the rafter will do the work with the 2x6 sistered to it.