Confusing transmission problem

Hey everyone,
I just recently started noticing this weird transmission noise coming from my tr-3650 in my 02 gt 5 speed. It began as a metal on metal scraping noise when 5th gear was engaged (not clutch chatter, the transmission was in gear fine and smooth). I had the tranny oil changed to Mobil1 ATF synthetic and had it filled to 3.0 liters/3.2 quarts, unfortunately this did not help in the slightest (although it did make shifting much smoother overall).

So basically I will be driving around and 1st-4th gear are quiet and smooth. Then I will shift into 5th gear and it shifts into gear smooth as butter, but there is this constant metal on metal noise that gets a little faster as I accelerate (it is still scraping while coasting). The other thing I noticed is that if I shift into 5th (from 4th) but don't let the clutch out yet, the noise will occur. This is the confusing part. Similary, if I shift from 5th into Neutral, but don't let the clutch out (keeping it fully depressed to the floor), the noise will continue, until I let the clutch out in neutral. This isn't shifter rattle as far as I can tell, as I have had friends listen in and they all believe its coming from under the shifter area.

Once again the car drives smooth as butter, and is not knocking out of gear/getting clutch chatter/etc. I feel like the tranny fluid change might have made it a little worse, but I'm not sure if it's just the placebo affect (and also this issue was present BEFORE I had the fluid changed). Any help is greatly appreciated guys.

After doing some research into this, I am beginning to think that low transmission fluid might be the culprit. I physically could not get my transmission shifter off to reseat it with RTV sealant, as the old stuff was holding like super glue. And it looks like Pep Boys (who did the fluid change) filled it through the top of the shifter (with the actual handle still there). My questions are:

1) Can I add some more Mobil 1 ATF through the top of the shifter handle and let it run down (will it still go into the transmission)? (BTW this is the Pro 50 aftermarket short shifter so I can see down the handle into what I believe is the transmission)
2) I can't get to the fill plug, so will it be safe to add 0.2-0.5 quarts through this method without the transmission having more problems?


EDIT:
Never found out what was bad, just replaced the transmission altogether, as a rebuild was going to cost as much as a professionally rebuilt one w/ a warranty.