After much experimenting, I found it best not to try to weld through the 'weld thru' primer as like you have experienced, it causes the weld to be contaminated.
What I now do for plug welds where 2 panels attach, is to spray the backsides of both pieces with weld thru primer, then clamp into position. Once everything is in place and ready to weld, I take a very small flat screwdriver and scrap all the primer off though the pre-punched or drilled hole where the plug weld will start.
Seems that once the arc is struck on bare steel, it flows out to the edges of the hole without issue, and the primer is still intact between panels for protection.
Note this is with MIG, I haven't used TIG so not sure how this will change things.
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Michael
Oshawa built 1 option Judge basket case. 463, SD KRE 295's, CNC'd factory intake, Cliff's Qjet, Stump Puller HR cam, RARE RA manifolds, Pypes exhaust, T56 Magnum, McLeod RXT clutch, 3.42 12 bolt. 24 year project almost done... 
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