Yes, I would gently wake her on your new schedule - I start by opening the blinds, doing little housekeeping chores in the baby's room, and then if necessary, rub her back until she wakes up. You do no not want to wake a child up abruptly when they are in deep sleep - gently ease your child out of sleep. And it's routine, routine, routine. I let my charge pick out his nap time pajamas, close the blinds, give him his paci and rock and hum (same song) for maybe one minute and he's immediately drowsy. We do the same routine every day for nap time and it could not work better.
As for the longer bottles, I give my baby charges something to play with while they are taking the bottle (babies around 8 months get bored). My 8 month old charge likes to tap the cap of the bottle on the bottle. Also, switch to faster flow nipples. I would never not feed a baby when she's hungry so all you can do if get her to feed longer.