This past weekend I replace the front pads. Both sets. Most of the time I use the foot brake and barley touch the hand brake. Occasionally, I've been getting a vibration when braking. Any ideas what I should check? Would it be the linked brake in front? Is there any adjustments I should be making? Maybe the pads just need broke in some more?
Clean your buttons that support your disks. Put a bolt through button and a nut on the other side and tighten gently. Now use brake cleaner while turning button/bolt combination until it turns freely. That should solve your problem and should become a regular maintenance item.
Depending on how old your discs are, they may have worn unevenly so that the new pads are not making full contact when you brake. If so, that will definitely get better as the new pads wear in to the contours of the disc. Allyance's button cleaning is a sound suggestion, and to that I would also add cleaning and greasing the sliding pins that the calipers mount on, so that the calipers can freely centre on the disc. You might also look at scrubbing the mating surfaces of the discs with a Scotchbrite pad to clean off any old pad residue.
I like to give the disks a going over with wet and dry when I replace pads to clean them up, and lubricate slide pins. I would also suggest you start working on changing your bad habit of mostly using the rear brake. You should reverse it or change to using both all the time. I mostly use the front, and use the rear only in hard stops (Together with front), or rear only to control front wheel lift or on slow corners to control throttle. Keep in mind mine are delinked. But even with the linked brakes, 80% of power is from front lever.