Hygiene - kids don't get it at this age. I'd put a reminder list in the bathroom (either written or with little icons, like pictures of a toothbrush and a bar of soap/dispenser) with a reward chart, and I'd have the dentist and pediatrician (and their assistants) talk to her when she's there.
Cleaning the room - it depends what you mean by that. "Clean your room" can be too general and therefore overwhelming for many kids. Breaking it down into manageable steps helps. Putting storage bins or baskets (labeled by category of toy) can help - we had a bin for Legos, one for toy cars/trucks, one for stuffed animals, etc. Some things were mixed in together (like all cars & trucks & vehicles, not separated by Match Box vs. some other brand/size) so there weren't too many categories. If her dirty clothes are all over the floor, put a hamper or a laundry basket in her closet or in the corner. If she can't organize the clean clothes, put dividers in her drawers or closet, even if you use old shoeboxes, so that socks are in one and underpants in another, tee shirts in a third one, etc. My son did well with a second closet bar at a lower height, and a set of those hanging shelves so that not everything was up high. A slotted divider from the office supply store can help hold books upright on a bookshelf so that things don't fall over if she takes one out. One on her desk can help organize homework materials like pads, library books, etc. A shoe bag (with see-through pockets) hung inside the closet door is good for shoes, but also for hair stuff or whatever else is on the floor. My neighbor put a towel bar on the back of the bedroom doors so the wet towels at least got off the floor and bed even if they never made it into the bathroom. Now, when you send her in to clean, pick one area on Monday (toys), another on Tuesday (stuff that goes in the shoe bag), another on Wednesday (dirty clothes into the hamper and the hamper into the laundry room.
Now, anything she can't find is her problem. So, if her good clothes sit on the floor or under the bed and she doesn't have her favorite shirt for Friday's school pictures, "Oh well. How unfortunate for you." If she pitches a fit, don't get emotional or start over-explaining. "How unfortunate for you that you decided to leave it on the floor." Also start teaching her to do her own laundry. When she runs out of clothes, she'll get the idea. There's no rule that a kid can't wear jeans more than once in between washings, or a wrinkled shirt. Let it happen.
Late getting ready to go to school? We solved that one in one day, by telling our son he was supposed to take the bus. If he missed it, I'd take him in when I was ready (not when he demanded it). I reminded him that late arrivals don't go to the classroom, but to the office to check in. I then added that he needed to explain his tardiness to the principal, and that I was sure she'd be happy to hear his explanation of why it wasn't important to come to school on time. That did it. I didn't yell or scream, I didn't threaten or take away. I just reminded him of the school rule. (If he'd refused to get ready, I'd have called the principal to give her a head's up that a quick meeting was in order with my son, and she would have helped out.)
So, my advice is to set a priority list, and address these problems one at a time, no more than one per week.