Sav... sorry it took me so long... I was gone all weekend. My wife was riding this weekend as well but thankfully didn't wreck.. I can't believe the heart dropping stress you went thru for that! I feel for you.
Bottom line is... you need to pull the entire front end. These guys already told you alot of cool ways to check. You can also check using a flat edge or level on the parts. But I like the more user friendly options stated above.
Once checked as stated above you need to reessemble everything. Sense you have the front end pulled... how old is the little ninja? If it has any countable miles 10,000 or more... grease up the neck bearings. Get the tripples back on and torqued to specs.
Now slide each fork in to the tripples. Make sure you get them in there even. You don't want one higher than the other. When you slide in the first tube... tighten the bottom clamp bolt. Not really really tight. Just enough to hold the tube in place. Now do the same on the other side. that should get the tripples lined up. So torque all four clamps on the tripples to factory specs.
Torqueing to factory specs is important. Especially when dealing with alum. You can get a decent torque wrench at Sears.
Now install the wheel and axle. Grease all that up real good. I just use axle grease... then re-install the brake caliper (which I usually string or wire up somewhere to keep the tension off the brake line)
Here's some pics of the last time I pulled forks on my 9R. I did them for a different reason... but the install is the same.
That's what you do to pull the forks... but if you have to pull the tripple... you need something else under the bike... like so...