A good resource book for you- The Pocket Idiot's Guide to Potty Training Problems (A praise-based program for reluctant toddlers) by Alison Schonwald, M.D., and George Sheldon. Here is what it says to do about your problem (pages 131-132):
"Continue your reinforcement of the expectation that your child will use the potty or toilet to make a bowel movement. It's not unusual for kids to insist on a diaper or Pull-Ups to make a poop. These kids are trained, just not for the toilet. Behave the same way you would if the poop were made on the floor: take the poop and the child, show the child that the poop must be flushed down the toilet, since that's where it belongs. If your child asks for a diaper so she can soil in it, start by allowing it. However, her jobs are now geared to make steps from poop in the diaper to poop in the toilet. For instance, have her job be to make the poop in the diaper while standing in the bathroom. She then earns her sticker or treat for that. A week or so later, have her make her poop while wearing the diaper but sitting on the toilet. With each job she does, she is closer to being toilet trained. Remember to give choices when you can: Which sticker to earn? Sit on potty or toilet? Diaper or Pull-Ups? She'll do a better job if she feels she has some control."
It also talks about kids making their bowel movements on the floor, so if this starts happening, this is what they say:
"Some reluctant children have been known to refuse to use the potty. Instead, they will go to the corner of a room, drop their pants, squat, and poop on the floor. Your first reaction, when you find it, is to go through the roof. There's a better course of action here. When you make the discovery, lead your child to the spot, and ask for help in cleaning up the mess. Take the poop to the potty, and have your child watch what you do with it. Have your child flush the toilet. Then say, "there, the poop belongs in the potty." No yelling, no screaming. Remain calm. Hide your emotions. (We know, easier said than done.)"
Sorry, but I just couldn't paraphrase as well as they said it! I just read this book a few weeks ago, because I just started the process with my daughter. I hope this helps. Good luck- it sounds like you are almost there!