Daytona Flat Spot

I dont know if you are familiar with downloading maps, power commanders ,ECU tune or the like.
When you change an exhaust the standard procedure is to put a new map/programme in the ECU to adjust the fuel/ air mix.( diy or dealer money)
Do you have the original pipe.
Sounds like your instinct says fuel.
How old is the bike? What condition? Throttle body rubbers perished? When was the last air filter, fuel filter change?Plugs? Coils?

 

As far as I remember (used to race these (Jack Lilley race team) there was no tunes for a race can on these models so definitely not helping.
These are probably the hardest triumph to set up as it was the 1st with keihin efi rather than sagem, plus they use a double butterfly system. I doubt any triumph dealer will know much about them (age related).
Your best bet is Clive Wood. He sorted one out just before xmas and the guy had been to loads of places.
btw They are crap below at low revs and the riders were told not to let the revs drop below 10k.
the 650 is a bit better but not much.
He is not too far from you at Swineshead.

 

I have a service manual but it is too large to upload (13Mb)...
I managed to download it free following a short trawl of t'internet

 

A free flow exhaust will invariably cause a leaner mixture and depending on how eco the ECU map has been set and how the lambda feedback is setup for closed loop running.

 

for a manual try this

https://www.manualslib.com/manual/1051857/Triumph-2003-Daytona-600.html

you can download or , as I have just done to check it out, just go through page by page

 

How did you get on?

 

T552
Agree Clive Wood is the man. He does all the 675 race bikes. Might be wrong but he has maps no deals has. And I think he actually tested the prototypes and the Norton's. If it is the same Man then he knows his onions. I have seen the work he has done to my boys 675. And JONO welcome to the Family
Family Ride Free
Joe