CosmicRocker, you asked about my technique for route map construcion/integration.
When a good panorama isn't yet available, I start to construct the mosaic using a very artigianal anti-vignetting tool (based on PSP illumination effect). Then I match images, normally using AutoStitch; lot of work is often needed to have a flat horizon; moreover, sometime, AS program introduce also a vertical distorsion (the image height is varing with azimut) so I need to correct with PSP again. Possibly, some rotation and local luminosity/contrast adjustment are needed too.
When obtained a good panorama, with a flat horizon and good overall uniformity, I englarge it's canvas in order to have a cylindrical map (horizon must lie close to the center height).
The panorama is then used as a texture in PovRay. For vertical projection, it is projected on a flat terrain 1.5m below the point of view. If rover is tilted, further adjustments are needed (pitch and roll angles). Usually, I make a 2000x2000 map with a scale of 10cm/pixel. Some fine luminosity/contrast adjustments are often needed, locally and globally.
Finally, the most difficult part is identify the location and merge with previous projections. Following suggestion from Forum members, I use as background a rescaled MOC image (like Phil strategy) and try to orient/translate the center portion of vertical projection on common features. Sometime, I use also some heading referring points for orientation (like far craters) because in the past I was accumulating orientation errors... (another suggestion from members!)
As you can see, is not an easy task; I have to dedicate lot of time on each step and sometimes results weren't fully satisfyng. For this reason, ironically, I enjoied recent Opportunity stall because gived me possibility to work on other tasks...