I'd actually agree that Timewalk is a bit pricey at 100$ a piece. Realistically it doesn't cost 50$ per SNES repro, (more akin to 20$-25$ if they've got a donor around). Factor in print costs for all the paperwork/boxes though, and that price a piece shoots up to probably 40-50$ a piece when averaged out...
Ultimately when you pay the 100$ you're paying for the time it takes them to go through and assemble the boxes, de-label and de-solder + re-solder their donors. I also don't know if they do profit sharing with their designers or not, so some of the $ might go to the guys who designed boxes/manuals, (or TW may just pay them flat amounts up front, I dunno).
Anyways... they could probably get away with charging 75$ a piece and still make some profit, but 100$ is a nice round $ number for them SNES wise and it seems to work out ok for them as they're usually swamped with orders. If it was too pricey they wouldn't always be swamped, right?
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To-do manuals: Arabian Knights, Gulliver Boy, Dark Law, Brandish 2, Flying Hero
Finished manuals: Neugier, Wonder Project J, Burning Heroes, Star Ocean, FEDA, Monstania, Chaos Seed