I did not. I Soaked them in cleaner and then lubricant like you do with normal maintenance, but I didn't pull the shields. I was working under the assumption that since the reel was not moved/activated while it was full of dirty water, that the sand and debris probably never had a chance to mechanically work itself into the bearing. I did spin each bearing by hand and they all felt smooth before I re-installed them. I work with bearings and mechanical assemblies for a living so I wouldnt have put anything back in that didnt feel right, but its been a while since i did that first re-assembly
I took it back apart over the weekend, and It really appears to me that it definitely is from the gears themselves and not bearing related. I couldn't pin/point any issue any further down than that, so am just going to send it in to DVT. I'm picking up my new boat this weekend and will be taking it on the lake with the previous owner(friend of mine) for a day of fishing, so it looks like I'll be picking myself up a new one. how unfortunate. LOL