Door post and rust repair

currently replacing door posts and lower cowl on my 93 fox. I fully separated the new doorpost via drilling all spot welds as i need to replace a portion of the passenger a pillar as mine has rusted and i didnt want to stitch weld around the entire a pillar. When separating the replacement post at the overlapping joints theres some pretty good hidden pitting i want to address before reassembling/installing not looking to do this job twice.

My question, im working with eastwood rust encapsulator plus that i plan scuff and apply to the undercarriage and cowl upper and lower and also the engine bay, those areas have minor surface rust and ive cleaned off nearly all the surface rust before applying. Would that be a suitable plan to apply in these overlap joints on the door posts? My only concern is obviously i cant weld through it nor would i want to and if i tape off all the spots for plug welds applying a weld thru primer over pitted rust probably wont last too long. Seems im going to have to cut out the rust and replace it with clean metal before i reassemble guess im just looking to hear thats what i gotta do
 
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I have used POR15 to coat the same areas you are looking at. Both on my son's 89GT and when I replaced the rockers on my F150.

On my F150 I fully coated the inner and repair rockers and then rosette welded through them. I did not notice any penetration issues. A little extra stinky smoke, but no functional issues that I have experienced.

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I have used POR15 to coat the same areas you are looking at. Both on my son's 89GT and when I replaced the rockers on my F150.

On my F150 I fully coated the inner and repair rockers and then rosette welded through them. I did not notice any penetration issues. A little extra stinky smoke, but no functional issues that I have experienced.
Oh perfect im glad to hear i ended up wire wheeling and lightly grinding down the metal shown in the photos and coated with eastwoods rust encapsulator ground down n sprayed weld thru primer on the spot weld areas im thinking about urethane seam sealing the over lap joints on the door posts in attempt to lock out the ability for moisture to get in smoothed down and painted over id highly doubt any eye would noticed other than my own once finished