The way that's worded, it could be taken a couple of ways....
Did you have the lower 1/2 of the factory windshield (with the top half taken off)..... or did you mean you have a 2 piece winshield with the top taken off right now (as in the roof you had has been taken off right now? If you meant you just took the top 1/2 of the 2 piece windshield off and you still have a roof is it hard or soft? And you say you lowered the back of the full soft top ( you mean you took the rear panel off or layed it down in the bed or something like it wasn't there)? Sorry, I don't have a rear panel so I don't know how it works.
I have a 2 piece windshield and factory hard roof. We are going riding again in a couple of weeks and im going to take the top 1/2 of the windshield off and see how it is... but I don't have the rear panel.