Wonderful to hear you (& your group) are still playing BKCII AJ.
Lots of us still are and some of the conversation has migrated to the Pendraken BKC forum now that Pendraken has taken on running the Commander rules stable.
Q1. I'd say yes. Stop and then occupy, as that is the situation normally with difficult terrain. Think of it that your troops would be cautious and not just leap in to a vacated enemy position !!!
The impassibility of an AFV Pit & Gun pit applies to a unit crossing it not moving to occupying it or defending it.
Q2. a good point that is being clarified in BKCIV. We always play it as per 1,000 points or part there of. Not popular, but I think that is the intention of the rules or you'll get into that 999pts v 1001pts argument
Same applies to any per 1,000 pts restriction in the army lists as well
Hope that helps ?
Mark