Read this tutorial: Headliner Tutorial
From what I can tell, you'll be just fine with a stock headliner (naturally the stock headliner will be too long on the sides) and the rear bow right where it is. The rear headliner panel will go straight back to the window opening, and the sail panel area will go down and away from the start of the curve of the rear bow.
There would have been a curved tacking area at the bottom of the sail panel area at the same height as the package shelf, but that's probably gone now after you chopped the roof. This may have been a series of metal tabs that held a piece of heavy cardboard to staple or tack to. You will need to attach something there again. Leave the rear window out until after the headliner is in.