Hi,
To use a "Standard checkout", the customer just use the common cart to add their products, and when checking out he can be able to select a payment method like "save my order" (which should be created by you).
This method will allow to place the order, but don't require any payments.
So thanks to your administrator interface, you can see the orders past, and manage them.
In the order details, you have the customer details, the products added, etc...
Then, you can edit the order, add, remove products, change their prices, and set another payment method in order to allow the customer to pay his order.
Regarding the wishlists, the email form has not yet been implemented. Originally the wishlists are used to be shared between customers, so there is no default email address for the email option. That's why at this time only a link is given, and this link can be shared. So for your needs, it will require some custom code.