Great project, and good decision to go with Holley EFI. One suggestion that I would make to you would be to try and replace the HP ECU for a Terminator X Max so that you can integrate the VSS into the ECU. A lot of my settings have conditions based on VSS such as the reverse lockout, fan cutoff and etc. There's not a easy way to integrate the VSS with HP ECU.
Otherwise it sounds like a great project. Looking back on all of my projects, one of the things I regret is not driving the car more. Before adding the turbo to the car, my suggestion would be to get the engine up and running with your current setup using cheap shorty headers or stock manifolds and get all the bugs worked out first. There are so many different obstacles and things to consider when doing an LS swap, and adding a turbo on top of that will complicate and prolong the build. Just my 2 cents. Looking forward to seeing the pictures of the build.
Ryan