Slide outs can be aligned. Sometimes they were not tightened enough when initially assembled and since have misaligned after being driven 14,000 miles. You would think the slide out would drop, but not always.
Another possibility is that if you have a wood floor, it might have been installed after the motor home left Jayco. The additional thickness of the wood floor could force the slide out that much higher. I believe the rollers of the slide out can be adjusted to compensate for the additional thickness of the floor.
I advise to take your rig to someone who knows how to realign it.
As far as water between the visors go. That is unusual. The water could be coming in from high above from the marker lights, or between the chassis roof and RV frontal cap above the cab dome light. If you don't know what to look for, have the repairman look at that too.
One thing certain, you want both fixed right away because water getting inside is a very serious matter. It will do BIG damage, and but quickly. Not just structural, but also mold & mildew.