Okay, some positive news on the Warp point front. The code is already written to support more Warp Points, so all I'll have to do is add them and they'll be good to go. I already inserted the one near the Alpha Skree and now I need to decide on two others.
I also figured out what happened with the Regenerator. Whenever you get a new Energy Tank, it resets certain internal variables. But I forgot to make it also refill Link's MP. So while it looks like you don't have full energy, you actually do. That'll be fixed in the next update, which I'll upload once I create two more save points.