You can handle the individual VAT for items by having a VAT column in your cart, you do not have to display this column but it can hold this individual value for each item in the cart. You will also need to create a calculated column that will calculate the applied VAT for that item by multiplying the VAT times the quantity. You can use the total price calculation as a basis for this. Then for the tax rule to apply the appropriate VAT tax you can just create the charged based on the subtotal of your total VAT for all the items.
You can assign discounts with codes in eCart, on the support page for eCart in the Solution Recipes section is one titled 'Creating a Coupon system for your eCart store'. This is a great example of this type of setup and may give you some ideas on how you would like to have yours.
For the custom ordering you have have a page that sends the user an email with Universal Email. Whatever processing you do in the scripts you can have the Universal Email server behavior send out the email afterwards.