I've had that sandwich plate rubbing before on a clevo/C4 combo. definitely worth checking. 
I'd also tip water over the fan/alternator belts, as silly as it sounds i've had them causing noises that sound nothing like you think

May be contact with a buckled sandwich plate. Don't assume it's the correct flex plate, make sure.   Yes, undo the nuts and see if you have some movement in the convertor on the studs. Should have 2 - 4 mm movement, at least. More could be an incorrect flex plate (unlikely, but possible).

Flex plate is new and I'm assuming it's the correct one for the C4.... Pioneer FRA-205.   Is it possible to check that without pulling the transmission off like undoing the convertor nuts and see if there's some movement?

Just listened to the video. I'm gonna say, that is the flex plate rubbing on the sandwich plate. Either the plate has a dent or buckle in it, causing it to rub on the flex plate and/or convertor nuts/studs, or the convertor is not fully seated and is forcing the flex plate forward to touch the sandwich plate. If you had this same noise before, something isn't sitting right there. The other cause could be using an aftermarket manual starter, which has a shorter snout, it could be interfering on the flex plate teeth. The factory used a spacer under the standard factory starter because the flywheel ring gear sits closer to the block rear face than the flex plate does. The whine I had in my C4 was MUCH quieter and more high pitched.

Never had any issues using headers (Tri-Y or 4 into 1's). I'm sure I DID have a dipstick and tube for a C4 somewhere, I'll have to have a look.

Not easy to find a good one plus isnt there a fitment issue with extractors?

This is what's done.

My advice (hard earned) is to use the FACTORY tube and dipstick. Do NOT assume an aftermarket tube and dipstick will read correctly (almost all do NOT). I know this from bitter experience. The AOD in my F100 always spewed out fluid from the breather at the 'correct' level, until I sourced a factory Ford tube and dipstick, to find it was almost a quart overfull. Now, no more breather spillages and no more frothing fluid trying to exit the tube when checking. Just my $0.02.

With that valve missing , the guy clearly has no idea what he is doing. What else was done to valvebody? Makes me want to question if pressure reg valve is fitted right or what else he might of F___ked up

Oh now that valve missing is a hug issue. How the hell did someone rebuild and leave that out? Just WOW !!!!!     With that missing it's a wonder it's not slipping.   As to oil level , be sure to verify the stick is correct. Run sting alongside tube and see where the "full" level is exactly