Looks like you are making some great progress there Jake
I am using the Silvertop Zetec engine at the moment.
The bell housing flange on the gearbox is about 25mm below the chassis rails & I altered my sump to more or less the same level as the flange.
Depends what the roads are like in your area, this might have an impact on the ground clearance you choose for your engine.
At the measurement I gave you for my install, the engine clears the bonnet fine ( Not sure if the Blacktop is taller than the Silvertop though )
Hope that helps