The last push-in clip (closest to the alt) in the harness clips into the alt bracket. That may be the one you have pushed into the fender? Do you have a lot of slack in the wiring harness behind the fender?
I would try unclipping it from the fender as you have it now, and see if you have enough harness length to pull the end of the harness over to the alternator, possibly even further back in case you may have skipped a clip somewhere along the way, while also making sure the harness isnt hung up somewhere.