Very interesting. Causation versus correlation... The misfiring is real, shouldn't be happening but it's unclear the role it's playing. I'd be looking at changing plugs in the near future if you're not sure how many miles they've accrued. Manifolds...we know from many threads over the years the exhaust manifolds tend to warp, mostly the right side, but most folks complain of a ticking when cold. I replaced my right/passenger side 2 years ago when trying to determine the cause of my dinking sound and discovered the #4 flange had pulled away about 0.025" compared to the others that lined up with a straight edge. I noticed telltale black carbon around the gasket area so the manifold was replaced with Motorcraft. It hadn't started making noise though. The popping...could it be unburned fuel/air mixture being ignited outside the combustion chamber? I had major misfire issues in 2013 at 80K mi, engine under load, but never had a popping I can recall. Plugs were shot. Since you're up on ForScan Lite, I'd be looking at both cylinder banks and comparing what you're seeing for Long Term Fuel Trim, #2 O2 sensors in each catalytic converter and VCT Advance and Error. The bank with the offending misfiring cylinder (assuming it's only one cylinder) may show a lower, maybe even negative, Long Term Fuel Trim and higher converter O2 sensor voltage but since the misfiring seems to be infrequent, it may not substantially affect readings. And monitoring all things VCT out of OCD and paranoia.
If it's the passenger side manifold in your picture, you'll have to lift the engine to get decent access to the nuts/studs. I got a NAPA engine support bar (barely long enough) and followed the procedures in the Ford Service Manual. You'll need to loosen the left side engine mount through bolt nut, remove the right side mount nut, remove fenderwell splash shield, drop the sway bar, remove starter, remove alternator, loosen trans mount nuts along with disconnecting the exhaust down pipes from the manifold and any other bit that inhibits raising the engine...I recall lower and upper radiator hoses and fan shield had to come off.
It would be interesting if it were a combination of the most difficult spark plug to replace with the most common exhaust leak location on the 3V.