I just lowering the Wifes 07 250ex. I used a kit from soupysperformance.com and it worked great. I droped the front of the bike 1" and have a little more to go if I needed it. I lowered the rear 1 1/2" at first. Raised it back up 1/2". Having the Adjustable links are the way to go.
Took a 1' off the kick stand and welded it up not to hard. The wife really loves her bike now.

 

Just did that 2 weeks ago on my wifes 250 - Just the rear links. Soupys links are def the way to go. Tried buying those cheaper links of ebay and they all suck. None of them actually lowered the bike.

Did you have to remove the front fender so it wouldn't bottom out?

 

I bought the lowering kit from soupys also. But I ordered them before getting the bike. I just assumed I'd need it. But it turns out I don't as long as I have my riding boots on.

I'm not sure if I should return them or install it anyway. Is it difficult to install?

 

I did not have any clearance problems with the front fender. I jumped up and down on the front end with all of my 240 lbs. It didnt touch. The install went really easy the only tools I needed were a 17mm and 19mm wrench for the rear. The front I use a 12mm and a 14mm wrench not sure of the allen wrench I used for the handle bars. The only hard part is getting the angle right when cutting down the kickstand. Any good welder should be able to though. The wife really love being able to touch the ground flat footed. She also said the bike turns abit better.