I understand your situation and your business need, but please understand that I am a business person too and must prioritize my efforts according to my own business needs. I don't make any money from your business and I cannot let myself feel pressured by the pressures you may feel that are driven by your business needs, I have plenty of pressure on me to accomplish my own business goals. I think it would have been better to evaluate WebStore more carefully whether it meets your needs before working on the site design (which looks really nice btw).
Of the things you mentioned, I might be able to implement the countdown of inventory by February, but the other things are not likely and some of them are not even currently planned goals.
The WebStore will pre-populate customer information from a previous order already but it is not planned currently to base that on the user profile or move that there, maybe someday but not soon.
The idea of having a way to make add to cart links in html content is a reasonable idea and probably not difficult but it requires some technical bad implementation because really I think it should require a form post to add items to a cart but we cannot use forms in the html feature, if you make it a simple get request (ie a link) it feels icky to modify data on a get request and actually what will happen is all kinds of bots that crawl the site will create carts by clicking those links and then will accept no cookie so they create a new cart on each request (of course bots can submit forms too but links are even more likely to create a bunch of junk carts). Still, even though it feels icky, I might do this because the benefit outweighs the ickiness required in the implementation.
Order tracking has to come after implementation of shipping so that will not likely happen soon enough for you. Once shipping is implemented we will add a way to mark an order as shipped.
As far as payment gateways we have support for Authorize.NET, PlugNPay, PayPal, and Google Checkout. If you need something different you should request it specifically what payment provider you need but I make no promise about implementing it.