You can create copies for the items that need different SKU and Prices and use Inventory Qty Adjustment to transfer items to new/different SKUs.
Say 1000 pcs of item AAAA you have in stocks, move to the action column under the Products and Services > dropdown arrow click Duplicate and enter details with new SKU and price quantity on hand 0, Name*- slightly different to original name e.g AAAA - Wholesale / Retail or enter with SKU and Save.
use Inventory Qty Adjustment to transfer items AAAA to AAAA - Wholesale / Retail / with SKU
The above solution will enable you to maintain the same items with different selling prices and different SKUs
Comment back for further clarifications / to discuss.