There are numerous ways to handle that. If you're really talking about that much inventory, though, I would recommend Magento. It's going to require a solid developer, though, and a dedicated server in order to run smoothly. That would give you a full-fledged shopping cart system which would handle sales tax, shipping calculators, discount codes, upselling and cross-selling, etc. Another good solution is WordPress and WooCommerce (which is what I typically prefer) but it may not do so well with as many products as you're talking about. If you're not looking for anything that detailed then you could just build a very basic form where people can fill in the amount they owe and submit a simple payment for that amount. This could be done with a standard payment button (cart upload command method) or via the Express Checkout API. You could also add Payments Pro if you're looking to take credit cards directly on the site as opposed to redirecting through PayPal for payment (although you'd still give PayPal / Express Checkout as an option for people). That's all pretty broad, but the question is pretty broad too, so hopefully that'll help some-what.
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