Yeah, first, how long did you leave the silicone to cure? I left it to cure for approximately 5 days. My beads were at 3/4in wide, even after 5 days, i think some part were somewhat soft than other parts, but I thought it was safe enough to start filling with water. As for scraping the old silicone, I scraped everywhere EXCEPT the silicone in-between the glass panels. On the corners, I put down extra silicone for extra protection/hold. I also used a credit card to "PUSH" the silicone into place, making sure to put enough pressure to go into the cracks that once had old silicone. IF i were to do it again, I would go with the spoon approach, sounds easier and less of a mess.
Remember the importance of resealing, HAVE LOTS OF PATIENCE BEFORE refilling with water. I would wait a week or week and a half before putting water in.
Good luck redoing it. I know it sucks, but it will all pay off in the end!