Good on you for giving it a go and taking one for the team Col.
I just finished applying an inkjet ink colour to a flame top Tele and was worried that using a rag for the clear top coat would soak up too much of the stain colour and just used a paint brush to apply the first coat of TO. Worked well as did the same approach on both of my Explorers over DT a few months ago as I was also worried how ragging would affect the outcome too.
Good way to get down the first coat that usually soaks up plenty without needing to rub it on. I have found that subsequent coats go on much easier too.