Jono, work on the basis that they did something or changed a setting from correct to an incorrect one.
My personal bet, is that the throttle body cables are now out of synchronisation.
Is the slight backfire present on 1100 twins, slightly more troublesome?
The left throttle body is the master body and the one connected to the computer via the Throttle Position Sensor (TPS). This is the little black box on the LHS of the left throttle body.
The TPS is attached to the butterfly in the throtle body, when you twist the throttle to a certain point, the butterfly turns and the TPS tells the computer that you are at position 69 out of 100, got that.
The right throttle body is merely a drone and copies the left throttle body via a cable. If the cables have been incorrectly adjusted the scenario works something like this.
The twisting of the throttle by you means that the left hand throttle body is in position 69, the TPS tells the computer that 69 is the correct correct position for both left and right throttle bodies. The trouble is, is that the right throttle body is actually on position 64 because the cables are slightly out of register with each other.
As a result of this, the engine either gets too much or too little fuel for that cylinder and every now and again it gets a bit of a boost because excess fuel is burnt in a rush and you get a slight surge.
At high revs the engine management is completely controlled by the computer and the slight butterfly differences are insignificant in the whole scheme of things.
I know all about these little imbalances as I do all of my own servicing/maintenance. I purchased a Twin Max carby balancer, it is extremely accurate and basically eliminated, totally, the kind of surging you are talking about.
I can tell you from experience that you only need a poofteenth of cable imbalance to get exactly what you are experiencing.
I will now tell you that it is also possible that something else is causing the problem, but I would think, going on what you told me, that it unlikely!
Mick.