Hi Bjarne,
different cameras or different resolutions shouldn't be a big problem; zooming between photos also works.
Issues which I find can be problematic in a project like yours are:
- very shallow incidence angles (as usually happens in the far field when using wide-angle lens)
- large differences between incidence angles (e.g. combining near-vertical aerial images with shallow incidence angle ground-based images)
- extreme differences in field of view (e.g., combining aerial overview images with close-up images)
I am not much of a wide-angle fan; actually, after some tests with moderate wide angle (24 mm equivalent), I prefer to work in the 35-80 mm equivalent range when I want to create 3D models. Of course I have to take more pictures to cover the same area, but resolution is higher and incidence angles are more similar between images.
Also, the letting-down-the-camera-into-the-mines part sounds like you require artificial light. Especially with relatively close-up and wide-angle images in narrow spaces with a lot of surface roughness (which I assume for mines), images taken with a built-in flash will likely cause problems due to shadowing and extreme illumination differences between images. How deep and narrow are the mines? I would try to create a relatively homogenous illumination which should be constant for the whole series of images (i.e., install a setup with several lights - e.g. on a tripod or on your PAP pole).
Working with different chunks for the different project parts (PAP, ground, inside) and later combining them based on ground control may be a good idea.