OK, I'm going to try and help you out here without making this too long. You have said a lot, but its not all correct!

The stroke of a 400 low deck motor is 3.38" and a RB ( 440) is 3.750. The deck heights are 9.98 vs 10.725 respectively.

A typical 440 piston is 2.061 inches. Take that, add it to the stock 400 stroke, add for crank travel and add in the stock 440 rod length and you'd arrive at 10.511 inches. That means the piston would be above the block over .500 inches.

Take your scenario and use the 400 rod ( 6.358, add for crank throw, and add in the height of a stock 440 piston and you would arrive at 10.109, which means the piston is still .11o above the deck surface.

What you are ultimately asking for is a 451" or 470" type of stroker motor, very very common.This would be a 440 crank in a 400 block, with changes made to the crank, piston and rods. The pistons need to be custom ( there are some stocking part numbers now however) because of the difference in compression height.

Adding stroke will have more of an impact on compression that will the larger bore. The larger bore helps in other areas however.

The stroker motor will certainly run better if cammed properly and especially in a heavy car. The addition of the cubic inches alone doesnt amount to a hill of beans. Its the additional stroke that creates the torque, which moves the vehicle. There are many other factors, but this is a quick explanation.