In view of the fact that you are going for a mid-engined config, you are propably right to lower the pan a full 4 inches. The engine (bay) will encroach into the cabin, and may necessitate a (lower) more upright seating position.
You have obviously worked on Beetles before and are no doubt an experienced man, but tread carefully here; Even in standard form the Nova is a difficult car to build, a mid-engined layout makes things more complex - you will be spending a lot of time in the garage.
My Build Pics: https://www.dropbox.com/sh/t4vj51udn...Beo_60GFa?dl=0
Thanks for the advice, I know it is not easy, and I will have a lot of work, but I am mechanic and engineer, and I hope I will can do.
I have the engine install, only have to do a middle support to finish, now I'm with the rear suspension and the mechanism of the gearshift.
The engine bay only will encroach into the cabin about 4" and without arrive to the rear window.
When I will have a little more advance the car I will open a post
My Build Pics: https://www.dropbox.com/sh/t4vj51udn...Beo_60GFa?dl=0