I'm also a short rider..5'6"..and can't flat foot the Ninja, so I know where you're coming from. One place to start is googling 'short motorcycle rider tips' or something similar and also going on youtube and searching for 'short motorcycle rider tips'...something like that. Lots of info out there written by shorter riders to help.
As far as moving the bike around the garage...when I need to move it forward I stand on the left side and grab both handgrips and walk it to where I need it. If i need to back it up (which I do every time I park it) I stand on the left side, grab the left hand grip with my left hand and place my right hand under the passenger grab spot under the passenger seat. I also leave the kickstand down when I'm moving it around....but I know some people try to discourage this...I find it helpful in case I were to drop the bike or lose grip it would fall back onto its kickstand.
Employees at motorcycle dealerships move bikes around all day...and they don't sit on the bikes to do it. They walk them around...you can, too.
Also when you stop you don't need to put both tip toes down...lean the bike ever so slightly to the left until you can at least put the ball of your left foot down or even your whole foot. Practice in your garage before trying on the streets!
Height is actually moot here, it is more of your inseam length that makes the difference. You can be tall with short legs or short with long legs.
That being said ihawk does state the proper technique for moving a motorcycle.
From the left side, grab the bars and push.
And since the kickstand is on the left if you have to let it down the kickstand will stop it from falling.
I leave it in gear and pull in the clutch when moving that way I can release the clutch and it will stop the bike.
Reversing the bike I will stand left, grab the clutch and put my hand on the rear of the seat to push, leaving the kickstand down and in gear.
As far as riding goes the Ninja I can touch but on my Vitpilen, which is way taller, I have to lean to one side at a stop, 99% of the time leaning to the left.
This keeps my left hand on the clutch, right hand free and right foot on the rear brake pedal.
And I always leave it in first at a stop, besides the ability to move quickly if I have to but also to eliminate the side to side shuffle from left side stopping, right side to shift, and back again.
Also if you can try to stop in the lowest part of the lane.