How do I set up a WordPress MU site using multiple databases? The site will become very large if it's all on one database.

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

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.

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.

Be careful when simply wrapping things into a mobile app. This can backfire on you and you could be presented with some very harsh edge cases. PHP isn't going to be encapsulated so much as the HTML/CSS/JavaScript. So keep in mind your mobile application could likely be in a position of requiring an online connection to work (because it must interface with your existing hosted WordPress site). This could also mean your hosting solution needs to be evaluated to ensure you can handle any increased traffic (and those traffic patterns could be different when coming from a mobile app that perhaps loads things the user doesn't see right away, accesses content that may not be cached, etc.). You want to ensure your server doesn't go down because then your mobile app would be "down" as well. That said... Things like Phonegap (web views) are a wonderful idea for utility apps because the performance is good enough for those (and hey even some games) and they end up being easily ported across many mobile operating systems. I would look into Phonegap, Appgyver (a new and totally awesome one because parts of it will utilize the native OS and your app will feel more responsive), Appcelerator Titanium, and perhaps even the new Famo.us one. Also take a look at the Ionic Framework for some further ideas about mobile UI and what you can do with these web view style apps.

Take the # of hours it takes you to do it and charge $50/hour. That's the price. Eventually you can charge $100/hour but that will require a bigger customer. If the customer is small < $1M in gross sales per year - charge $50/hour If the customer id medium < $1-5M / sales - charge $75 Over $5M - charge $100 The challenge you'll face is clearly defining the expectations and handoff so that you're not stuck doing stuff that you can charge for and always getting interrupted from past customers.