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Dang, Im hella vertically challenged and like my stock Road King with the seat. Flat footing is a non issue for me since I can never get both feet on the ground. I just use one foot. I would recommend building your confidence in riding and knowing your surroundings and foot placement instead of worrying about having both feet in the ground. You will also build more leg muscles. I know it looks embarrassing getting up and walking your bike but my ego doesnt bruise very easily
Have you considered the more narrower primary cover? That might work
I'm just a smidge shorter than you and had my King lowered as well. Had my stock seat done (lowered and narrowed) by Mean City and got flat footed when sitting on the bike. I also have a C&C solo seat. It's a tad higher than my stock seat now, but it's also a bit wide for me. I got the C&C seat narrowed and it's great for me now.
I have 11.5 shocks on my RG with front lowered 1". The seat I shaved down the sides to lessen the width of the straddle. Also shaved the height off the seat about a 1/4" or so. I'm 5'6.