I am very familiar with this type or upright type windshield as I have owned two FJ Cruisers and they both were susceptible to chips and cracks, therefore, I purchased a windshield brakeage insurance\warranty because with these not only the windshield replacement is costly, but the installation...
Have they provided a substitute vehicle or are they paying for a rental while your vehicle is in the shop? They should, according to the warranty. If not, this must be demanded from dealer and/or Ford. If they are, then you're getting a vehicle to drive at no cost to you, therefore, you're...
have you checked the clips on the cowl piece? When I first picked up my Bronco one of the clips that hold it down was broken, so it had to be replaced. If it's not secured down and you open the hood, the hood will catch it and pry it up and break it.
Can the backlight work if the pods are connected to the Aux switch power? If so, how do they alternate between the two modes? Does the wiring harness have a separate power wire that may be able to attach to its own Aux switch so that it can be toggled to either color?
I ended up having a professional installer do it along with installing the kick panel speakers. $150 was a good deal I thought especially with a torn rotator cuff. I installed the front and rear 4" speakers myself.
Check your setting for the blower selection(ie. front, footwell, defrost). Mine did this awhile back and I had to reselect( a couple of times) the blower selection to front only. Don't know why this caused it, but it worked and has been okay since.
Easy to install. Was not able to drive over 50mph, but the noise level was lower than with no mesh top at all. Panels went back on easily. I think it improves the look inside. Here are are a couple of pictures from front and back after the panels were installed: