I have A 450FSR,the impression I get is that.Wire diconnect=more responsive throttle with less fuel economy(race mapping).........Wire connected=unresponsive in first halve of throttle with better fuel economy.(emmisions mapping)
My yellow/blue wire connected is together with a black wire attached to the EFI control box via eyelet and bolt.This suggests that leaving it connected is grounded,and disconnecting it is ungrounded.By putting it on a switch and grounding that to the engine you arn't changing anything accept the location of the ground.
IMHO you need to disconnect and leave it tapped up.My bike didn't require a re-trim and if you were to connect it and re-trim you would just end up with the same mapping as having it disconnected.
On a side note running the bike with it connected is more fuel efficient and fine if you are on the road and your bike can cool easily.But what I found was that in the tight singletracks on a hot day I had over heating issues if I was in the tight trails for too long.This suggests that the emmision controlled mode just leans the bike out to get better fuel economy.