After lots of head scratching & pulling it apart & re-assembling it about 4 times, I finally figured out it was the clutch primary gear rubbing on the side case.
It was where the boss is for the large oil seal. As I mentioned earlier the baffle plate had signs of being rubbed by the wet clutch, so I stupidly bent it back inwards slightly to make sure it cleared the clutch gear rivets.
What I didn`t realise is it actually supports the side case to a certain degree.
Luckily I had another unmolested one to fit, this one I tweaked slightly outwards this time at the rear end.
After fitting the case again & trying it everything`s okay.
Oh yeah, I also noticed that the water pump nylon gear was cracking on the large boss on the bearing side. Thought I`d replace it with the one from the wet clutch cover but, you guessed it, that one was cracked also.
I had one more in another wet clutch cover this one is also very slightly cracked but is the best of the three. Have fitted it until I get a new one.
Just got to pull it apart one more time to put back the best gearbox oil pump!
Thanks for your replies people.