I've been gathering information and mulling it all over to see what to do next. On the cat issue, from what I can gather, aftermarket are never as clean as OEM and the OEM's on the 100 are twin cats per bank where I now have a single high flow cat per bank ...
Having a single 200 cpsi cat per bank plus the headers would account for a lot of extra noise as well, OEM cats tend to be quite restrictive.
I've spoken to Charlie and he says that after research it probably needs twin cats per bank (fair play to him for saying this) which he has offered to have it back in to fit or he also suggested having it tested on LPG now that's up and running and sticking with single cats for performance. I've read on the net that some sports cats need to be really hot to work properly so I'm going to book it in for an emissions only test and give it a really good thrashing beforehand and see what the result is before making a decision on that. It's possible the tester didn't get it anywhere near warm enough as they just look at the coolant temp gauge as a guide. If I can sneak it through with thrashing and additives I would settle for that.
Charlie has also offered to have another crack at the noise problem with (based on a phone description not a drawing!) a double decker main silencer, so the gas does a 180 out back along the side and a 180 into a 2nd stacked silencer. The OEM silencer was HUGE so there should be room for this, we'll see.
I'm always a bit cynical about likely follow up service when things start going wrong and assume it will be a battle / none existant because that's what usually seems to happen but actually Charlie sounds determined to get it so I'm happy with it so I will try again on the 25th but ask for an extra tail pipe as well so I can carry on experimenting with the supertrapp if I need to.