Yup, you have to isolate/identify the spot that rubs. It sounds like you have already carefully checked the frame/pillar/line guard assembly. Any one of the pillars in the wrong spot or not seated can skew the frame. Assemble with even force--no more than a good fitting screwdriver can apply comfortably snug--in a crisscross pattern. Eventually--once certain the assembly is true--you will want to reinstall the screws one at a time with a dab of mild formula threadlock, nail polish, or poor man's nylock--a shred of plastic wrap or 6x tippet.
Other than that, a lot of guessing. A warped spool face can be observed and straightened with judicious thumb pressure or tapping.
Little changes in the conversion might contribute. The bevel of the backplate-mounted pawl under the drag plate needs to be reversed by rotating it 180 degrees. The plate should be clean and fit freely but flush under the spindle mounted bearing. A sloppy fit there--sludge or grit in the way--might cause a scuff.
Most common in Pluegers--and inconsequential--is the Pflueger scuff on the spool plate side facing the backplate. Just the slightest inward pressure, natural when winding the reel, can cause its surface to rub on the brake shoe. If the the latch, its grove, or the frame bearing are slightly dirty or worn, slight side to side play can increase the scuffing. Cleaning and light lubrication with fine machine oil usually takes care of that, maybe a check that the plunger latch is straight.
Most likely--and simplest--the brake shoe is slightly askew. Sometimes its spring is fit crookedy, angling the shoe away from the frame. Sometimes debris or sludge under the shoe is holding it high. It should move freely when the spring is lifted. Also, changing winding direction will sometimes put the shoe working against an old wear pattern for a while so the shoe is forced up against the spool. It's mounting pivot favors RHW so it can take some wearing in to LHW.
Great reel. Worth tinkering.
viewtopic.php?f=4&t=9843&p=62689&hilit=Pflueger+scuff#p62689