Hello Luke,
Great you have it all running and now (after your run in proces) you can give it a full go
With all the good tips you will be getting, you still will find out that the 3ma is difficult to set up.
And that your setup (probably) will be different too other 3ma's (regarding the exhausts you are using)
Just try to feel the engines needs, is the best tip I can give you.
And with feeling i mean understand the behaviour of the 3ma engine.
It will have a difficult butum and mid range (speciualy when you have removed the VAJ system)
There are tricks to try to loos that problem zone (as Ndwedwe and Edd are writing)
-Playing with the airjet size is a good one (most of use use the airjet in the range 100 till 130) mains will be different to witch air jet you will be using-Using a different Needle jet (stock 3ma's have Q8 and Q9 in them) when you use a Q4 (from 3ma3) it will lean out that difficult zone more.
(3ma3 needlejets in combination with
3ma1 needles) -And Removing the Balance tube between the reed rubbers (use alu plugs to cover up the holes) will help in that difficult zone (Edd this could be something to try fore you

I'm riding with it. Until now works great.
(As on the low rpm's the mixture will not be sucked to the other side, making it richer)
So the Manny combinations with the above mentioned tricks/ideas, there will hardly be any 3ma the same.
Regarding your PV problem you could try to loosen the pv cables a bid and see what happens.
They shouldn't be to tight, and pressible by finger
Its just a thought.
Keep posting your findings, and let that 3ma sing
Cheers