Two things:
Tools are grayed out when customizing. Can we not customize them now?
It seems obvious, but I've seen the starter house turned into the real house by Isabelle. Will talking to her also fix houses you might have messed up by giving clothes or fossils or whatnot?
Which tools are grayed out? If it's the axe I believe it can't be customized. also some can be grayed out if they're too new