In regards to the integration, the Integration Bus
was created just for this reason. I'm not saying it's the easiest thing to program/learn but it is pretty robust and works well once you figure it out.
I've also done 1 way pushes into kentico using custom tables and scheduled tasks. For instance if you have changes that happen on a regular basis you could write these records from your product management inventory system to a custom table within Kentico. Then create a scheduled task to run every N minutes/hours to process the records in Kentico and update the SKU information via the API.
In regards to the updating of the SKUMinItemsInOrder and other dynamic fields based on customer agreement. My guess is you will need some sort of linking table(s) like CustomerAgreements and Agreemenets. Agreements will have the defintiion of discounts, purchase requirements, etc. and the CustomerAgreements will have the simple IDs in them. There are global event handlers
you can use to perform additional check, events, etc. You can also look at the E-Commerce guide
and the Developers guide
for custom providers. These should give you what you need for info to get started. I'd also suggest downloading the API documentation
if you haven't already.