Setting up problems with products that have heaps of variations

Setting up and managing that number of variations with just the core WooCommerce plugin will be very difficult.

Have a look at this plugin.
http://ihayag.com/jaf/woocommerce-too-many-variations-plugin/

You might also want to look at an add-ons plugin to substantially reduce the number of variations:

http://codecanyon.net/item/woocommerce-extra-product-options/7908619

http://codecanyon.net/item/product-options-for-woocommerce-wp-plugin/7973927

http://www.woothemes.com/products/product-add-ons/
http://docs.woothemes.com/document/product-add-ons/

I cannot say whether they will meet your needs – you will need to make your own judgement.