I'm glad things started moving again! When it comes to the wafer overlapping, have you tried cutting the hole in the wafer off center to move it away from the incision? It works for me.
I had emergency surgery a month ago for a small bowel perforation, and the surgeon gave me a temporary ileostomy. Up until a few of days ago, I also had a lot of stoma pain, especially after eating when the stoma was moving.
When I changed my wafer the last time, I noticed that the stitches around my stoma had long strands that were getting stuck under my wafer, causing it to pull. I took a scissors and carefully cut the ends shorter. It really helped, because I haven't had any pain since.
If you're too scared to cut them yourself, you can always ask the nurse or doctor to do it for you. Until then, you can smooth the ends of the stitches around the stoma, so when you put on a new wafer, they won't get caught under the sticky part.
I think the pain is a combination of the stitches pulling and the area around the stoma is still healing. I just wanted to assure you that the pain will go away.