Hey Jack,
Thanks for detailing your issues here. Points 1 & 2 are a piece of cake. So is the size issue actually! Using the Out of Stock is indeed your best solution here as it will give you all the functionality you need to manage this operation smoothly. For instance, we can limit the amount of pre-orders per product in case you're not able to have large volumes done within limited time (by the way, when you say you're able to alter sizes, do you mean taking an existing item in size 38 and turning it into a 40? This is important to know for how we'll manage inventory). Also, you can mention exactly when the out of stock product will be shipped, right on the cart page (see the cart screenshot on the Out of Stock's app page for an example).
We'll also need to make sure your notifications are set up correctly so that you can let customers know when their item gets shipped (this is especially important if you have people ordering a mix of in stock and "out of stock" products, as you will need to easily notify them when the out of stock ones get shipped).
By the way, I'm based in Paris, so we'll be able to work in real-time! Just send me an e-mail at michael(at)m36webdesign.com and we'll get started.
Cheers,
Michael