Sounds like a combination of things could lead up to your issues.
I once thought it sounded crazy to remove a whole quarter panel to do patches & mods on it & then have to weld it back on. Welds & patches done in plain sight & out in the open areas of panels are far more critical than welding near and along a seam & bodyline. Welds running parallel with & right near a bodyline are both stiffer & easier to hide less than perfection.
Ghost lines can occur on very solid repairs. Simply thicker or thinner material in an area will expand & contract differently though solid, as will panel bonded areas that are really solid. Saying it again, these same areas in a better chosen spot near the right type of bodyline, such as between a corner bend & another bodyline are so much easier to hide & stay hidden forever.
First up , I'd suggest coupon sized samples of same gauge & type material & do a practice run replicating basically how you've been welding &grinding. Now you can check backside & bend test. Probably need to just back up & reschool yourself accordingly.
Yes, we can't always be perfect on repairs & a dip inwards on a weld is better than it being a high spot that grinds thin & flexes. Better filler on critical area helps. I recently got VPA for the first time in about 25 years. It has similar consistency of jb weld, but stiffer through expansion & contraction, not being an epoxy. Good improvement for shadow prone areas. Don Hutton also mentioned USC carbo fill , which has carbon fiber strands as an option for bad spots. Haven't tried yet as would have to mail order.
EDIT:: you said lap weld as I was typing. I'll be blunt. If you were my grown son. I would spank you about now. BAD......... Butt welds only or it's your butt.
Out in the open , they WILL shadow every time.