Eagle BIFs and URGENT AF-S question to birders/tele shooters/trouble shooters!

In less than a week, I'm leaving on a trip to eastern Hokkaido, Japan, to shoot some white-tailed eagles and other birds, but I'm having a strange problem with my 300/4 AF-S. I bought it second hand a couple of years ago, and it was perfect, but I recently had the AF-S motor replaced, and now the focus seems to be all messed up. I'm hoping somebody has some insight, and fast!

First, I will show some shots I took at this Hokkaido location last year, where my gear functioned perfectly. See the following post.

Julie