An interesting idea. I know what you mean about there being no genderswitch stories for RK.
On that note, I have a few nitpicks:
'…Yep, she was right - wait a [minuet]!'
'Damnit they were almost at the door! “W…WAIT A [MINUET]!”'
You've misspelled 'minute'. As you have it in these cases, 'minuet' is actually a type of dance (or maybe it's a style of music... I'm a little fuzzy on the details), not an interval of time.
'The two travelers did, seeing that where Gohei had been sent headfirst into it there was a great big [floor].'
I think you mean 'hole'.
Also, one thing you mentioned was bugging me. You say that fem!Kenshin is wearing scandalous clothing, and I get that you're trying to make her different from canon!Kenshin, but I can't help but feel that this goes against her character. Kenshin is a very modest and self degrading person, so showing off all of that skin kinda contradicts that. Besides, this is Meiji Japan we're talking about, considering that this was set during a time where, in the West, women wore high collared dresses and it was considered scandalous if you could see their ankles, Kenshii would be drawing more attention from what she was wearing than if she hung a neon sign above her head that said, "Hitokiri Battousai is here." Not something she'd enjoy, I'm sure.
Not that I'm saying you have to change it, it's just something I thought you might want to think about.