The back right wheel is where the alternator and timing belt are. I am not familiar with the noise a VVC makes - people say it is noiser than a standard non-VVC TF.
Ignoring the VVC aspect, I hear a sort of knocking and a whirring in one of your videos. Of course without being there I could just be picking up on ordinary engine noises exaggerated by the camera, but I'll assume what I think I hear is real.
I have a slight knocking at idle on my TF 135. It is coming from the timing belt cover. I determined this with a mechanic's stethoscope. I believe there may be a clash between the timing belt and the cover, but it strengthens and fades over periods of something like 3-6 seconds. I tried STP oil treatment at first as I thought it was a shell bearing in the bottom end but the STP made no difference as I poured it in and as I said the stethoscope test I did later showed the noise was coming from the cam belt cover. It is completely masked by normal engine noise if the engine is revved.
As for the whirring noise, the alternator is in the same area as the rear right wheel - you can get to it with that wheel removed. I'd have a quick look and see if the alternator belt is OK. Also, you could rule out a worn bearing on the alternator by loosening the alternator tensioning bolt so the alternator belt can't drive the alternator. The car should run OK without the alternator for a while. Don't allow the alternator belt to get caught in anything.
As far as misfires and rough running go, my first port of call would be to replace the spark plugs (and inspect them for condition and appearance). Then replace the two ignition HT leads (relatively cheap IIRC), although you could try messing around with WD40 on them and moving them about to see if anything improves (not guaranteed though). Finally you could replace the two coil packs if the first two things don't work, but they're more expensive.
Spark plugs and HT leads don't last forever so it's a good idea to replace them anyway. Make sure you get the right HT leads (and coil packs if you change them). I found GSF car parts gave me the wrong ones despite me giving them my reg - the ones they gave me were too deep (VVC?).