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.
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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.

Thanks, as always, for the advice and feedback!