If you still have the old suppressor fitted in the ignition lead then take it out as it isn't need in this day and age and it just messes up the ignition anyway.

If you haven't split the crank case to clean it and it was pretty gunky, I'd be tempted to run it with some cheap oil and do regular changes until most of the movable crap is out. I split one of my cases down that looked to be pretty clean and found the sludge traps were well and truly full. It's said that modern oils with detergents can wreck an older engine by pushing the gunk through the big end if it's not been stripped and cleaned but it's not totally true, the cleaning agents carry the carbon deposits away but don't tend to remove the gunk that's built up in the traps.

As for not running well, sounds pretty normal to me, well at least that's how mine run.