Thanks for the very detailed review.
You're right about the E and R keys. That's why I added the alternative push/pull controls (X) back in a day. Regarding the holding Shift key, you can toggle the always run mode in the options. I.e. you will be walking while holding Shift key.
In fact I'm working on the extended version of Nymphiad with lots of improvements, new levels and improved old ones. Definitely going to add checkpoints in the long levels there. Hope that I'll manage to finish it this year.