Obviously you have a crush issue now with the end gaskets. Putting on the scraper raises the pan way from the timing cover and rear main , so if it was not good to start with, it will now be worse.
If it was a job I was doing, I'd probably look at trying to get some crush back on those gaskets first, before trying to fill a gap that shouldn't be there with silicone.
But if you don't have the tools etc to do that, then you may just have to use the silicone and cross your fingers it won.t leak again.