Use 0000 steel wool to eliminate the surface rust. There may be some discoloration, but it won't affect function. Lube lightly and keep it scrupulously clean.

You did not say how you cleaned it before you put it away after using it last, but i would not follow that procedure again. I would do what Ed and FirstBubba said and then instead of WD-40 i would use Sheath, a penetrating oil that is thinner than weasel piss to wipe it down for storage. Store in a low or lower humidity location if possible. Before use again i would oil the required places with Remington Oil with a occasional re application as needed during use.
A final thought might be to talk to Kimber to see if they have any specific products/procedures they recommend. My Nephew has the Kimber with the .22 conversion and loves them. Happy shooting.

Those stains might not even be rust spots, but dark patches of packing grease. Try wiping them off with a rough cloth before hitting them with steel wool.

After all the above was said and Done!...Run,Jump or Drive to your Local W*M and get a Bag of "DampRid" and put it in your Gun Locker,Safe or night stand, to Eliminate excess Moisture from all your TOYS.

A word of caution about stripping a Kimber in the "II" category. Most have the Schwartz-type safety, which has a small protruding part on the slide that needs to be handled correctly so as not to bend or otherwise bother it. All my 45's are Series 70, so I can't tell you exactly what you need to do, but I'm sure the manual will address that issue.

Also, while we are on the subject, Google "idiot-scratch" and read about how to prevent it. I use a small piece of clear plastic from clam-shell packages as a shield.

Dallas, don't be discouraged with your Kimber Custom II. I've got one and I'm very pleased with it. I keep it clean and it performs reliably, accurately. Don't drown it in oil; it need only be very lightly lubed (like any other autoloader) and it'll do a great job.

WD-40 is actually water soluble so I wouldn't use it as any kind of protectant against moisture. The stuff is about useless in my opinion. After cleaning I wipe my guns down with 3-in-1 oil. Can be had at any hardware store. It's the most amazing stuff I have seen yet for keeping the gun safe in harsh weather conditions. If it'll hold up through a day of tracking in thick snowy brush or goose hunting in a hurricane, I'm sure it will hold up just fine in your gun closet. Of course, it's too heavy for working parts in the action and I have never used it in the barrel of rifle either. Inside the house in normal not-so-humid environmental situations (i.e. not the deep South or eastern seaboard) I have never had a problem storing well oiled guns in a foam gun case. However, DO NOT leave cased guns in the trunk of a car. The temperature changes outside during the course of the day will cause even a well oiled gun to develop rust.

Dallas- It is possible that you need a solvent. Try lighter fluid. That stuff dissolves a lot of greasy stains, including glue.