"Does it hook up with the westen side of Shepherds Pass???"
I haven't been into Center Basin and cannot tell you how the trail is on that side, but it definitely connects with the Shepherd Pass trail at a feature named "The Pothole" on maps. It is visible as you ascend/descend the Shepherd Pass trail. I have talked to a couple of hikers who had used the trail and they had difficulty following it up to Junction Pass from The Pothole, frequently losing it in the brush down low. Personally, I think it would be hard to get very far off route, as the trail goes up a valley. The beta is to stay to the right(east) side of the valley going north, and to the left if you are coming south from Center Basin. Also, you might want to check with the rangers on the current bear situation in Center Basin. It was closed to camping several years ago after a couple of hikers got injured trying to keep bears away from their food. It may have quieted down by now, but it wouldn't hurt to check.