Pictures would help. But if I understand your question, you could always go with a thin piece of molding at top of cabinets. On mine where the soffit meets the top of the cabinet they finished off with a small piece of trim (like a mini crown molding) at the top. Also on the side with no soffit, I like your idea of running the cabinets to the ceiling.

I have a similar dilemma. Along one wall, we have a soffit that can't be removed but along the other two walls, we would like to remove the soffit. I like the idea of 42 inch cabinets, with no crown molding or just a small subtle piece. Good luck!

I would be very cautious about getting the 42" cabinets if it's going to significantly lower your cabinets to the point where you are losing space between the countertop and the bottom of the cabinet,. Also, 42" cabinets I can be a bit of a problem if your ceiling isn't even. I think some companies make 39" cabinets which might be a good compromise. Almost to ceiling with a bit of scribe molding for adjustments.