I don't know if going to a manual 0non-powered) master cylinder will help. Have you measured the room you need
Are you running aftermarket alve covers such as the spacer that allows you to bolt on legacy valve covers? That added height is probably the issue, as there are thousands of LS-x swaps in Camaros and Novas with no room under the hood as well as Cheveles and B-body cars without any one mentioning an interference issue.
As a slide rule and book of logs trained engineer I was taught to find out what the problem was first before I attempted to fix anything. Still applies in our digital age.