Part of the deal with Two-Up ride is to crank up the shock preload and if you have air valves in the forks to add a bit up there too. It is easy in the spirit of the moment that you are not riding solo and heel that bike over a lot without counter leaning to allow the bike to stand up straighter, with your body on the inside and feet pushing on the outside peg/board...ground clearance is not good when you lose 2 or 3" fully laden with passenger and gear.
As a more permanent solution...new Progressive or Air Shocks will allow you the preload adjustment to gain what you lose with Two-Up riding...but the front requires a Progressive stiffer spring change, slightly thicker oil, and perhaps air valve/caps to put up to 10-15PSI to gain an extra inch adjustability. You might want to determine what is hitting the hard deck and gain about an inch by adjusting things up and inwards to allow larger lean angle, but your solo riding experience has already probably eaten up most of that...i.e. I cut 1/8" rubber off the jiffy stand bumper and gain about 3/8"on left, as it tucks in closer; rearranged the exhaust clamp holddown hardware and gained about 3/8" on the right.