I haven't bothered looking at many WIPs lately, but Nice Work!
If you want to get that timer operational, there should be a copy of my Majora's Mask clock engine somewhere on these boards. You'd just have to remove the day limitations and change the speed, which is easy since the code is all commented. Come to think of it, the clock's frame in your screenshots looks an awful lot like the one I drew.

Some other old examples I made could be easily upgraded for a newer GM with better coding. You mentioned having certain items or characters work with targeting - that was the 2nd ever thing I made with GM. It included a dynamically updating order for multiple targets based on distance & priority, and an optional feature that makes Link's movement curve around the target, but that part would have to be re-written to work with your movement code.
If someone can figure out how to change sound pitches in GM7, I could remake the 1st thing I made with GM; an Ocarina engine that was only good with 5.3. You could actually hold and bend notes, record and play back, etc.
Also, this is the same thing I said to TRM many years ago: I think the shading on the Temple of Time's teleport pad is backwards, because there's a big light source coming from the door.
