I bought the bike a month ago, and same as your wife, I couldn't flat foot, just about 1 1/2 inches short. The dealer where I bought the bike from were able to find the lowering kit and they added in for me for free (around $150 part + labor). I also bought a HD boot with 2 inches heel, great boot. Now I'm all flat foot and already put in 500miles on my bike. Put in boot insole for additional height.
lowering a bike is always an option. what you do when you lower the rear is increase the rake of the forks. This will tend to make it heavier going slow and make if feel more stable going fast.
to keep the geometry about the same you could also lower the front by letting the fork tubes rise in the triple clamps about 1/2 to 3/4 of an inch. Depending of how much the rear link lowered the bike it might get the steering closer to original for a lighter feel.
also you will have lower ground clearance when lowering a bike so test that slowly till you know the limits. The ride should be about the same because one rarely bottoms out the suspension unless you load it down with gear.
The stock CTX kick stand allows the bike to really lean over so maybe you did not have to shorten it but in most cases you do. When I had to, I purchased a new kickstand, sawed an inch out of it and had a welder put the foot back on.
the boots were a good idea, and you can adjust the foot controls to fit your boots a little if needed. you could also take your seat to a shop and have them narrow the front some which would help you putting your feet down.
I have had to lower my VFR800, made all the difference in my comfort and confidence.
Happy riding.