2012 Bonneville Handling Issues

Is it just the wheel sizes that have been changed or have the forks been changed as well?
If original forks then may be a new 17" rim laced onto your existing hubs.

Can you post a few photos of the bike, it might help other members offer advice

 

When using a lowering kit it is advisable to lower the forks in the yolks by a small amount to maintain the trail and rake and hence maintaining the bikes handling. Fitting an 18" wheel will have raised the front and unless the forks have been adjusted to compensate the trail and rake will now be different. I read somewhere that lowering the front makes it easier for a bike to turn in so if I were you I would lower the front forks in the yolks probably by about 10 to 13mm and see if there is an improvement. I think there will be.

 

There could be a lot of other things causing the issue (tyres, poor suspension set up etc) but assuming they're ok, the Bonnie is a sweet handling bike on the 17" wheels (better than with the bigger diameter wheels).
So I'd say either switch to cast wheels and get the advantage of having tubeless tyres as well or, if you want to keep the tubed wire wheels, get a 17" rim put on as Samsgrandad suggests.

 

And of course check your tyres aren't underinflated.

 

If the larger front wheel is causing the issues you could try to find a smaller tyre? Assuming the profile is a 100/90 then a 100/80 would get you within 2 or 3mm of where it should be. I don't know how common a profile like that is though and could be a problem trying to find an odd size.

 

Didn't that model originally have a 19" front? I'm sure the T100 did, for example. The alloy wheel 865 Bonnies like mine (SE) were 17" front and rear. Is it the 865 engine? What model is it, exactly?