Maybe I am missing something (pretty likely) but if the OP sprayed WD40 on the chain and ran it through the gears, how did any WD40 get inside the freewheel? Unless soaked from behind its not clear to me that there is any issue (whether or not you agree with WD40 as a cleaner/chain lube). I would expect the majority (if not all) of the WD40 ended up on the floor, in a rag, or in the chain links but not in the freewheel body. Same idea with the bottom bracket.....getting WD40 on the outside of the BB and/or cups isn't the same as spraying WD40 into the BB....so again there should be little to no issue.