tracing water leaks is always a pain. ive spent many times in a boot whilst being hosepiped and sometimes its not where you would think.
but yes finish the repairs and then see .may be sorted.
dont be putoff too much by saying that the youtube guys are way better than you. they do jt for a living and have all the gear but it certainly helps to give guidance and ideas.its only bent metal after all and its taught me many things, the main being ' dont try to make a repair section out of one piece if you cant.often its easier and neater to make several profiles .
the areas you are now doing are typical omega ones ,rear of sills,inside door shut,inside arch behind plastic cover,inner panel (to seat base !) but as ive said many times ,omegas dont rust anywhere as bad as most 60's-80's cars and never to the point of being unrepairable.