Depends on what type of riding you do. If you go hard in the dirt I have heard that the lowering links reduce the travel.
Most dirt bikes are taller than the KLX.

 

 

City riding I would get a supermoto. They can go down a trail ok, don't take them on ST.

 

 

I have a 30" inseam and the KLX is too tall for me . If your a hard cord dirt rider leave it alone you don't want to screw with the suspension , Lowering it affects the geometry and compromise's the suspension , Having said that I have the super motto version and still dropped the suspension 1" so I can flat foot it , And have nobbies on it and take it in the dirt and on trails , As long as I'm not going crazy it's ok off road and does fine on ashpalt , Sitting at a stop sign or backing out of parking spots I need to have my feet on the ground , Works for me...PS I like the Super Motto look with nobbs on it

 

The problem is all in your head(confidence) unless there are balance issues.
I have a SF but cranked the rear shock preload pretty high and use a slightly larger rear tire at 130/80-17 vs. 130/70-17 OEM size.
This makes the un-laden seat close to 35 inches high like the advertised S mode seat height. This reduces bottoming the shock, wheelies are easier, and ground clearance is greater
for curb hopping and loading dock drops.
I have no issues at all at 5"-7" tall and 31" inseam. With boots I can touch both toes well at stops. Sometimes I just slide my *** to the side and flat foot
one foot down usually with the right foot on the brake pedal. I have never dropped the bike on the street and only once on a mountain jeep trail.
Having owned a Honda Magna 20 years the super-moto(my 1st) was a big change but I most likely will not go back to cruisers ever again, except that restored 1940 Indian Sport Scout I saw in Craigslist was interesting.
Perhaps riding mountain bikes where touching the ground is not possible due to my 40" saddle height has helped.

 

 

Up front first - ride it as is and remember, it is virtually never a need to be able to touch flat footed on both sides at the same time. If you tip you only need the foot on that side touching down. If it is an issue getting on the bike, you simply hold the front brake, then step up on the left peg and put your foot over to the right,then sit down. I even do that on my street bike - keeps me from hitting the seat or tail section with my right foot. Try it for a while then decide. For what it's worth, I'm near 65 and stand 5' 6" with a 32" inseam crotch to ground, wear 29-30 pants, a bit low. So it's not like I"m some limber kid.

I've ridden a KLX 650 with a 33" or so seat height for 19 years/50,000 miles without lowering it. I thought about it, but the soft suspension let it settle so I could tip toe the ground both sides. Not flat footed, but I have no problem with that. I found I virtually never sit flat footed at a stop, even on the street bike. Usually one foot, knee bent, on the ball of my foot. Problem with the 650 was more about how top heavy it was. If it got leaned over too far I had to lay it down, get off and pick it up. This sucked. Then when test riding an 06 KLX250 for my brother (it was near me, he was 120 miles away) it felt like riding a mountain bike. Incredibly light, regardless of what anyone says. It's all relative. So I found an 09 and bought it.

My brother, who is around 5' 8" actually lowered his bike, then after riding for a while, raised it back up. I never bothered. Again, I can touch with the ***** of my feet and that is fine. The bike is so light it is far less problem when on a trail as well. So with a 32" inseam to the ground, I find it no problem since the only time I need to actually touch down when vertical is at a stop and usually only put down one foot even then. Once moving at any rate of speed touching the ground with both feet is totally irrelevant and useless for me.

I'd say consider the KLX250 if you find one you like. Then if you only need drop a couple inches slide the fork legs up in the triple clamps as far as possible and either buy or make a set of lowering links. (Making them is easy. Block the bike up on a jack so the bike can be raised or lowered a bit. Remove the stock links, then lower the bike the amount you want and measure center to center on the mount bolts. Make a link from flat steel stock to that size. A couple bucks worth of steel and maybe a drill bit.) Just don't drop over around 2" or you will have the tires hitting the underside of the fenders on full compression.

But I'd recommend if you have enough riding experience and confidence in your riding, try it at stock setting start. You may find it isn't worth doing, as did my brother and I.

If I did lower the bike more or less permanently though, I'd put travel limiting spacers in the fork and shock, maybe do the valving at that time as well. It does the job right and is reversible. You keep the proper bottoming stop distance so it won't hit the inner fenders. If you stay with stock springs they will probably be adequately preloaded as well, definitely the rear since it has adjustment.

This is my opinion based on my experience. Some like to be able to sit flat footed. That is fine, a personal preference. So don't take this as being some negative trait, just that you may find, as I have, that it isn't important to you. You only know if you try the bike out first and for a while, not just a day or so. Get a chance to see if it becomes comfortable.

Edit:
You could back down the preload on the shock a bit to have the bike settle a bit. You could probably take an inch off the seat without much problem in comfort too. The suspension will sack out a bit from new and doing the step on peg mount thing will make that easy. As for backing up and all on a trail, really not that bad and I find I usually get off a bike to back up anyway.

 

I have my pre load set to max as well ,And a slightly higher Seat Concepts seat , The bike fit's me perfectly . Chubby you can get a custom lowered seat that are pretty comfortable, Snappster whats your trick for wheeling the SF ? Mine doe's not wheelie unless I throttle up and drop clutch ,maybe my teckneak is all wrong but it won't power wheelie at all , I'm an old guy and have been into bikes for 50 years and my knees are shot from wheelies gone bad over the years , maybe I'm too tentive from all the damage , Anyway like I've said whatever works for you ...