I've noticed under the edge of the cab up behind the running board where the sheet metal is welded I'm getting some pretty nasty rust starting. Its to the point of bubbling the paint, so I need to do a fix to clean it up and stop it.
Around the 2 holes is what I'm referring to, any suggestions on the best product to use to clean this up?

 

Spray on, or roll on if windy, asphalt undercoating.

Not much else you can do.

 

For that area I would spray it with a product called Boeshield T9. It's a penetrating oil/wax material developed by Boeing to spray into the nooks and crannies of their planes to prevent corrosion. Very popular with bicycle/motorcycle racing crowd for chain waxing. A couple of coats dries to about the luster of a wax candle unless buffed when applied. I just sold my 2003 FX4 on Monday with 100k miles. The undercarriage did have some rust but for the most part looked pretty damn well preserved. I'm getting an early start with the stuff on the new 2013 XLT I bought to replace it. Hope you find this helpful.

 

REMOVE the rust FIRST, then spray with a product of your choice. If you are planning on keeping the truck for a while you need to to some serious undercoating and rust protection otherwise the truck will rust out in a northern salted climate.

 

Take it to a Ford dealer. Ford has a corrorsion / rust coverage for 7 years 100,000 miles I believe. they may cover it.

 

I noticed a spot of rust on my hood near the grill on my 2010. I took it to the dealer and they repaired it right away. I'd definitely try that route first.

 

Lowes and Home Depot sell something called "Naval Jelly". Works wonders to eat away rust. I've used it on my bumper a couple times. I would look into what a previous poster stated about fords rust coverage. See if they take care if it first.

 

That only covers penetration, not surface.

 

POR-15 works great if you follow the process like you're supposed to. I've used it a couple of times before on minor rust that was starting on doors and it didn't come back.

 

I have a 2010 and live in Northern MI where there's lots of snow. Zero rust. The key is to take it to the self serve car wash and spray off the salt at least once a week. You need to wipe down the door jams too. I had a 01 Excursion that I just sold that was also rust free. The key is maintenance.