When I switched Sadie to 2 feedings a day I weened her off by feeding her less for her 2nd meal each day and would add the amount that I took away to her 3rd cup(she eats the same amount as yours). I did this for about a week but I still seen some changes to her bathroom breaks. Which I would say is natural. She will come around though. Sadie eats her supper around 6:00-7:00pm every day and doesn't have a bowel movement until after she eats her next feeding which is 6:30-7:00am. She will go about 3 times during the day though so she makes up for it!
I would try very hard to not give in to her whines at 3-4am. You know that she should be able to go at least 7hrs before she has to pee and I would say just as long, if not longer for the other as long as she has just enough room in her crate to lay down. Obviously if you give in to her whines you will be getting up every day at that time!
Also, I took Sadie's water away at 8:00pm for a long time and have gradually extended that time and am now to 9:00pm and she will be 9 months old on the 21st of Jan. I don't like this for the sake of her being thirsty throughout the night but it has helped and prevented her from whining in the middle of the night to be let out. Eventually I will give her water in her crate but will add just a little to the bowl and gradually add more until I think it's safe. Sorry, I'm ranting... Good luck with Lacy! You will find all the information you need on these forums... I have been very grateful to have found this site.