After months of trying to get this to work, we came up with a solution that works for us. The Customer Pricing app will not work when syncing the inventory with LightSpeed Cloud. The Shopify variables get overwritten when inventory syncs. We uninstalled Customer Pricing. I got Bold Apps to create a private section on the website for our wholesale items that only registered customers with a specific tag on their account from the built in customer management of Shopify are able to see the wholesale items. If someone finds their way to a wholesale specific item, they are presented with a registration form and have to be manually approved. http://shop.sweetwaterbrew.com/pages/wholesale
Items that are only available to wholesalers are added to the wholesale collection. For items that are sold to average customers and wholesalers needed a little workaround. We used boxes of items to sell to the wholesalers in bulk, while breaking those boxes down within LightSpeed as individual items with standard prices for our main Shopify site.