If image alignment is such a big problem when scanning film, I could have a solution to this: I wrote a program to blend RAW files with different exposures focusing on:
1. Maximum noise reduction: each individual pixel is taken from the less noisy RAW file
2. Avoid any progressive blending: final pixels are taken from one single source image so any loss of sharpness due to misalignment is not possible
To avoid artifacts in the border areas taken from one or other shot, some configurable progressive blending can be set for those areas. It usually does not represent more than 3% of the total image surface.
For instance this HDR scene (12 f-stops of real DR):

was built noise free from 3 RAW files 2EV apart. Each pixel was taken from one of them according to this blending map (black colour represents the highest exposure RAW file, gray is medium and white is the least exposed RAW file):

A tutorial with an approach to do the manual tone mapping of the resulting image is also included. Sorry for the crappy English online translations.
ZERO NOISE TUTORIALHDR TONE MAPPINGPeter, if you provide me with 2 or more RAW files shot over the same film at different exposure values, I would be glad to blend them and show you the result.
BR