Hello Alvaro:
For some reason Photoscan does not find as easy to align NIR imagery as it does with visible.
I have tried too many times doing the same flight mission alternatively with NIR and Visible cameras. Same camera-lens combo, same height, same, day and almost same time... no matter what I've tried the fact is that Photoscan always succeeds orienting visible while very often fails with NIR datasets.
IMHO the problem comes from the lack of contrast and crispness in later photos. Take into account that most lenses are designed to deliver good images for visible wavelengths, therfore, most of them suffer from all optical diseases one would like to avoid (comma, chromatic aberration, focus point shift...) with regard to NIR radiation. It usually doesn't matter as hot-mirror filter cuts away NIR but... this is not gonna be the case of your modified camera.
Sometimes you have lenses that produce NIR images that are well focused in the center but are completey blurred near the borders, this is the case you most probably have, so make sure a particular lens works well before paying. Hot-spot is another very common issue; just take care!
Focus ring scale becomes useless and I see no rule behind that behaviour: In my beloved mZuiko 12mm, the lens is decently focused at infinite when the scale index is at 2m (yes, two meter equals to infinite
!). On the contrary, in my Voightlander Color-Skopar 21mm the infinite focus is shifted in the opposite direction to a certain point beyond the infinite labeled mechanic limit of the ring, so I cannot get foccused photos at all but stopping down aperture a lot which carries worse problems on board of a plane.
So, I can say it is almost mandatory to have ground control from geo-tags as
a priori help for Photoscan to align. Even in that case, you will likely find some photos not getting aligned that will need some "hand-work".
Best luck
PS: If you found a good lens whose rendition was good enough both in visible and NIR with reasonable angular, please tell me.
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