A couple of things come to mind. When installing a mechanical seal ,"Cleanliness is next to Godliness" It doesn't take anything caught between to seal faces to cause a leak. The whole purpose of having seal faces lapped to 2 lightbands is to prevent anything from migrating in to the interface of the 2 seal faces.
There's a Youtube video inserted by PaulD in a previous topic on mechanical seals and it's a 2 part series. The :"mechanic" who produced the videos is a bit of a hack but goes in depth as to how the job gets done. He makes a very interesting comment in the video about how easy it is to bend the water pump drive shaft and how people he knows had to set up the drive shaft in vee blocks and dial indicate the shaft and straighten it. Hopefully this is not the case here with your issue but something to keep in mind.
You'll have to tear down the water pump again and have a really good look and maybe at that point with some help from a buddy, spin the engine over and see if the water pump shaft wobbles.
Here's a link to the topic and you can watch the video from there. Not sure if it's the first or second video where he talks about the possibility of bending the shaft.
Mechanical Seal Topic
