You need to get down to solid metal or you're just wasting your time. At least there are replacement quarter panels and patch panels available for the J series Wagoneers, but for the wheel well area, you'll have to fab the pieces yourself. Don't skrimp on the patch... all of the rusted area has to be removed. Hopefully your HF welder has gas capability... otherwise, see if there's a kit to add it... you'll get better results than with flux core wire.
There's a full-size forum at Jeep Forum
that might be useful to you too.