Congratulations on it turning out to be a relatively simple fix!
I feel both your pain and your relief. I thought I had a duff 'box too, hence my trip to Mackies to see if a fluid & filter would solve my troubles. The car was clunking under load, starting very slightly in 5th a couple of months ago and then proceeding to affect all gears over time until it got so bad the car was undriveable.
Turned out it was a misfire. Should have known really as I had just changed the plugs a day or so before it got
really bad. Convinced myself though that it couldn't possibly be my brand spanking new plugs. Took them out. Checked them. Put them back in. Took them out. Put in the old ones. (I can now change all 8 plugs in 40 minutes, bonnet open to bonnet closed
)Still misfiring. In the end it turned out to be one of the rubber insulators on the end of a coil pack had a very small tracking mark on it. My disturbing it had obviously taken it from being a minor ailment to causing a complete misfire. BTW - no fault code on either VCDS or SnapOn Solus Ultra diagnostic unit.
Quick method of identifying troublesome cylinder(s):
Loosen the clips on each coil pack so it is still connected but easy to slip off
Now with car running, have an assistant turn the wheel slightly to put load on the engine. Car should now misfire as per your issue.
Disconnect each coil pack connector in turn. Misfire will worsen on good cylinder, no change on bad cylinder.
Wish I'd done that 5 minute job in the first place instead of spending a couple of weeks panicking and worrying about phantom 'box problems . . . . .