I'm back for a while.
Hero, I'm glad you decided to work on another Super Metroid run. Your route is a very interesting one. I also considered to use a very similar one before, but later decided to go for Plasma anyway, mostly because it shows a more powerful Samus in the end and because the boss fights won't be too long that way. Due to my tests the total result for both routes is almost the same.
Here my script file for both routes:
Any% route comparisons between Draygon first (Plasma route) and Ridley first (Spazer route)
And a couple of test smv's:
Draygon last (Skip Plasma) route to go
Draygon last (with Plasma delay, for faster Mother Brain fight)
Both show that the Space Jump is of very much use in this routes. I think it saves more time just in this Maridia areas alone compared to the slight delay to get it.
Skipping HJ Boots seems to be a more interesting option. Due to tests I got a ~700 frameds delay (with skip of the e-tank of course) in total, and it's indeed doubtful if this 700 frames can be catched up during the rest of the game,
IF it wouldn't be for the big Shinespark through the large room before Draygon that easily saves this time and most likely even more. Without HJ-Boots you won't be able to walljump up the vertical room fast enough to keep the charge for the Shinespark.
Non HJ-Boots Shinespark attempt to Draygon (failed)
I was around 5 frames too late to start the Shinepark and can't see a way to cut them down. If it's possible, skipping HJ Boots could be a interesting choice (or if a Gravity Jump could work here at least, which I didn't test though), otherwise it's out of question as well.
Even for the sake of comparison it would be very interesting to see which route (Plasma with Ridley last or Spazer with Draygon last) would be faster in the end, so I would be very interested to see what you, hero, can do with your route.