Something to consider with a WMS is how the product and variant relationships happen. We completely mapped the Shopify format within SKUSavvy mobile WMS for Shopify so that they will match.
Another thing to consider is Shopify rate limiting if you have 1000's products to consistently update. Another challenge that you may run into is being able to fulfill partial orders when one variant is back-ordered. For this, you can split the order into separate shipments, and fulfill the product that is available at the time. Having multiple fulfillment options does make this more complicated.