I like the idea of selling the fabric by the pound. Most quilting cotton will weigh about the same.
That also makes it easier to price smaller pieces and scraps. I would put scraps in one gallon zip lock bags and price each bag the same. No opening or mixing bags.
FQ could be priced by the each or you could bundle them in groups of 5 or 10.
Precuts, if in originally packaging I would price at 50% or less than the original price. You can check online for approximate prices.
I would not offer to cut yardage. Too much work and you give up display space to set up a cutting station.
Books and magazines, depending on how many you have to sell, either bundle the magazines and sell that way or price by the each, but only have one price for books and one for magazines.
Thread, put similar colours in baggies and sell by the bag.
Tools this could be more of a challenge, but you could have one price for rulers up to 6 inches in any direction and another for rulers over 6 inches in any direction.
Try to find all the accessories for each machine and sell as is where is, no testing.
UFO, WIP, PIGS, if the pattern and supplies are easy to identify, bundle them up and sell them too.
Having the quilting sale separate from the main sale is a good idea. Invite local, and not so local guilds to come shop.