2004 Heritage with 4.2L, manual trans 140k miles, RWD.

Whenever I apply brakes to come to a stop, at about 30-40mph until I stop the steering wheel and even the seats shake. I've got pretty aggressive snow tires on it but I don't recall if this started when I switched to those.

Highways speeds, 70-75mph, has a little vibration in the seats but I attribute that to the rough/loud tires. I've checked the wheel bearings (try to rock the wheel vertically in and out) and they seem fine. Replaced upper a lower ball joints & control arms on both sides a year ago too.

The only thing I can think of is maybe warped rotors?

 

rotors

 

Yeah, rotors.... especially if the shake is in sync with your steering wheel.

 

Check your caliper slide pins before replacing rotors. I would remove pins and completely clean out anchor plate holes where pins slide. Use silicone grease and lube new pins and use new boots. Frozen or poorly maintained pins could also cause vibration while braking.

 

Good idea. Yeah I usually grease the pins every time. The whole truck is pretty rotten so I'm sure those boots could be replaced.

 

If the pins pull out and look ok then you probably can reuse them. I would use a can or two of brake clean and clean out the pin wells. Maybe taking off the anchor plate to do a good job of it.
Use a thin bladed, long shank screw driver or something long and thin and a cloth or a pipe cleaner to make sure all the old grease and dirt is out. Motorcraft has a kit with new boots and rattle clips, part # BRPK-5624 available at Rock Auto.
RA also has the Motorcraft Silicone Paste XG3A. Torque setting on the Anchor Plate bolts is 136 FT-LB. Torque setting on the caliper bolts is 21-26 FT-LB.