Two things:

1. Woah, I never really thought about it, but the not disrupting your perception of consciousness thing is huge. Not only do they have to replicate all of the electrons and neurochemicals in the right locations, but they also have to ensure that their motion continues in exactly the same way.
2. If they’re able to do all of that, why the fuck does anyone ever leave a transporter dirty? They clearly already do some level of this with the bio-filters. Same with teeth, why don’t the transporters keep your teeth sparkly and your breath fresh?

Bonus points:

• Are water-based showers a luxury? Surely you could just slap a replicator in there and not have to worry about plumbing.
• Speaking of plumbing, I can’t recall seeing a toilet in Star Trek. Even if there are, they’d just have a matter decompiler in there, right?
• So, why not just use the transporters to clear your bowels then? Can’t shit your pants on an away mission if you got cleared out on the beam down.
• Like, why can’t you just roll out of bed, hop on the transporter pad, and show up to your classes at Starfleet Academy having had a Shower, a Shit and a Shave on the way!