Wordpress theme development

There is a lot of points in your question which unless someone has the exact same setup as you - I don't think you will get the answers you are looking for. I believe you should limit it by asking yourself: What is the ONE thing the MLM plugin I am looking for can do so that it achieves the maximum amount of result to my business by using it? IMHO - it would be the ability to set commissions for the products you sell and award commissions to those affiliates that actually earn you sales. All other features, while nice, are ancillary features that from the perspective of the affiliate - don't really need in order to be successful. In that regard - I would suggest https://affiliatewp.com/. When it comes to running affiliate programs on WP sites, it wins out as the best in my experience. Hope this helps! Glad to assist any further if you need help.

Pricing for different tasks that require the same amount of time from you tells the Customer (and your subconscious) that you're working at a 5 on task x, but working at a 9 on task y simply because it costs/earns more. That seems to be a disconnect. Your time is your most precious asset, and I would charge for it whatever you're doing. If you build a site, and they are happy with your dev fee, but feel like you should charge less for SEO, simply let them find another SEO guy. That's their choice, but YOU are worth $xx.xx, no matter what you're doing. Also, in general, take whatever you're charging and add 10% to it. If you're still busy, add another 10%. Let the demand level determine how much work you do, and at what cost.

Yes. https://docs.woothemes.com/document/configuring-woocommerce-settings/

Well first off I wouldn't recommend trying to power your client's database with the standard WordPress database instance. They can use WordPress for the website all they like. But with millions of records like that, you really don't want to move those data in with WordPress. For that matter, you're probably gonna want a dedicated database server to answer those questions, if the client doesn't already have one. You might also need to investigate something like Elastic Search, depending on what your search requirements are and what sort of database they are using (pay close attention to whether or not it provides full text search ability). Beyond that, and somewhat obviously, you're also gonna want SSL on the website and to make sure you're up to date on federal and state privacy requirements for data like this, as well as best practices for securely transferring data over the web (port configuration, ssh keys, etc). The privacy concerns would raise a flag for me. If those data have anything personally identifiable in them - which they very probably do - then you're really gonna want to make sure you do your research on security of personally identifiable information. Government specific privacy /security /auditability requirements may also apply, so double check that too.

Checkout is a high-quality WordPress theme by Array built for marketplaces of any kind. https://arraythemes.com/themes/checkout-wordpress-theme/ Let me know if you have any questions about implementation, and I'd be happy to setup a call.