OK, first up:

You've gotten a lil gun-ho there huh? ahaha!

Now, I don't mind discussing some parts of the RP, but I also prefer to let other parts play out rather than micro managing every detail like that. (like crikey, down to the potion ingredients aha!)

he would know Phyr is there because she has heightened senses, course if he minds his own business she won't pay him much mind till stuff starts getting hectic. As long as he doesn't have sticky fingers and doesn't loiter she won't care. She's got better things to do.

Now;

Ayaka is selfish. very selfish. If you all come into her shop causing a ruckus she will kick everyone out. She doesn't tolerate stuff like that. Hell she barely tolerates it from her sister and that's her flesh and blood that is.
She wouldn't let them/him hide in her shop whilst the operatives look around. She'd ask the operatives how much they're willing to offer to pay, and likely give them up, or hide them if they would pay more. She is shrewd. Money talks.

The other parts of the story I am fine with! Just pointing out some of the things Ayaka would do in those situations.