I used a combo of old Costco card and fingers. You're right, it did tint up a little, but I didn't notice any "disfiguring" or pulling of the stain, so I'm happy with that. Below is from last night, shortly after applying the second coat of filler.
This particular body doesn't have a lot of flat area, so the fingers come in handy. Like you, I haven't been too worried about getting it real smooth, the sanding seems to take care of that quite well. And yes, I've barely made a dent in the pint of Aqua Coat, I feel like I could get a lot of mileage out of it.
I will probably do one more coat before applying the decal and then several coats of varnish.