04 Bonneville - Ran Lovely- Now Misfires Low Revs

If you changed the pipes you need to check that the jets are correct. Standard size for oem exhausts are 110, aftermarket pipes may go up to 115 or even 120.
That is a starting point, together with an ultra sonic carb clean.

 

@Mark Sansom @Tim Gibbs has answered you question handsomely

 

Hi Mark,
I had similar problem recently on my 2014 Bonnie, I decided to remove AIS completely and fit plug kit with ECU (fool plug) fitted. I am 77 years young with replacement knees and it took me 53 minutes from start to finish. This very much improved slow ride jerking. Then I removed rubber air snorkel from side of air box. Made perforations about every inch all around the inside tube section. This allowed a lot more air suction without using Bellmouth. Also keeping the front of the snorkel to stop water ingress. Then checked and cleaned spark plugs and set to .09 mm. Increase tickover to 1000 to 1100 rpm. After all these simple jobs were completed I put 50ml of STP in tank with 3 gal fill up. The motorcycle now runs like a Singer sewing machine as smooth as silk. The only problem is I’m not sure which single fix did the trick but is was fun doing them all. If you need any more help or photos etc let me know.
Stay Positive
Walter