Elite does and I would guess has done the most work on them.... Midwest Diesel does a fair amount as well. Side action Does them. D&J precision is doing them. Tons of shops do. Any reputable machine Shop will honestly do it for you for the $$$. If you're looking at bigger valves you can do them but if you want the biggest valves possible you are limited by the size of your bore on your pistons/cylinders depending on what that is.
Typically head porting is $500-$800 for hand porting, CNC porting is typically well over $1000+, I know D&J charges $1500 to do them. Oversized valves im not sure as that involves new valve seats and a valve job so that will probably depend on the shop you use.
The main Problem is 6.4 head castings are inconsistent and usually thin and if you're not careful you'll punch through the casting walls and into the water jackets.
People are doing 1000+ HP on stock 6.4 heads....myself personally I'm making almost 900 on fuel on a stock port head. A lot of people would rather leave them alone and just use nitrous to make the power rather than risk ruining a set of heads because the port job went bad.