I do think the front will still be higher than the rear with the engine in. I think the flip kit usually results in a 5 inch drop. It may come down, but I dont think so.
On the rims, I believe they recommend 16 inch wheels or larger for the spindle drop. Other than that its the wheel offset. I have just the 3 inch spindel drop on my choptop now, and dont notice anything rubbing, but that is with aluminum aftermarket rims.