So, I was going to do a SM64 120 Star Speedrun but I am not comfortable with the Through the Jet Stream Star in JRB. Can you simply just change the route to have JRB being placed between BitFS (Bowser in the Fire Sea) and WDW (Wet Dry World) or do I completely have to re-route it.
You would be able to do that, although it might be better to do JRB after Vanish Cap because you would have Metal Cap by then, plus you'd already be in the lobby for CCM. Ba-da-bing, ba-da-boom.
You would go to WF before JRB anyway, although you would have to do both slide stars before Wing Cap
Otherwise, the route would be mostly the same. All you would have to do is just change your split names to accurately represent how many stars you have at a given time.
All in all, it would probably be worth to just practice perfect swimming. You do it again in DDD after all (as long as you don't spend the time to get metal cap by the sub).
For the beginner route, you can simply replace JRB (16) with CCM (16), but just remember that you have to do Aquarium during CCM (16). And JRB can be done later as JRB (59).
