Bump.
No emulation issues are resolved still, but I did find out something else: it's possible to get 9 clocks initially in What's Cookin' Doc, rather than 7. What do these two clocks mean to the route? Quite a bit, actually. About three moments of era-changing are saved.
I updated the route to below:
Stage (Clocks, Golden Carrots)
Start (0, 0)
Nowhere (1, 10)
Wabbit on the run (10,32)
Guess Who Needs a... (11,37)
Hey, what's up, doc (20,54)
The Big Bank Withdrawal (26,69)
The Greatest Escape (1) (30,80)
What's Cookin' Doc (1) (39,104)
F. Red Pirate Road (1) (42,107)
When Sam met Bunny (43,109)
The Planet X File (57,135)
Objects in the mirror.. (61,150)
The Greatest Escape (2) (63,154)
La Corrida (64,159)
Vort X Room (68,159)
Witch Way To Albuquer.. (69,167)
What's Cookin' Doc (2) (73,179)
The Carrot-Henge Myst.. (81,199)
What's Cookin' Doc (3) (83,200)
Wabbit or Duck Season (84,200)
Magic Hare Blower (98,231)
The Carrot Factory (106,246)
F. Red Pirate Road (2) (107,252)
Mine or Mine? (117,293)
Downhill Duck (118,293)
Conquest of Planet X (119,307)
Train Your Brain (124,328)
Hub Golden Carrots* (124,333)
*hub Golden Carrots will be collected in between stages, not necessarily at the end (that's time-inefficient, not to mention impossible because 99 carrots is the max you can hold at any 1 time)
**The revisits (marked with (1), (2) etc.) are necessary due to these stages requiring spells to get all clocks. These spells can only be obtained after visiting these stages at least once.
***Empty spaces inbetween level names indicate switching times. Yes, that happens surprisingly often.