You have started from the wrong end of the problem i am afraid. You should have said- "which scanner is stupid enough to allow me to have complete control over the motor at all times?". instead you have said (in a very round-about way) "i have a particular scanner, can i make it do this?"
The answers to the first question are many and varied. The Cardscan 800c might work but is quite small and has only one resolution, the fujitsu S300 could be convinced to do it, but the calibration is poor, and its CIS (not sure if the cardscan is). Other backend authors here will have ideas on good scanners. The second question can best be answered by someone who spends some time looking at the source code of the hp_rts88xx sane backend (which is not yet included in sane) to see how much control you have over the initialization and calibration steps. the obvious contact there is the backend author, see http://hp44x0backend.sourceforge.net/ i hope this helps. allan