Your tool kit has a spanner, a rear shock adjusting C spanner and an extension handle for it. The allen key and screwdriver are attached to the bottom of the seat, the other tools should come in a plastic wallet with a rubber bungee to attach it to the underside of the seat.. Front axle is 14mm...
Not really sure where you're struggling, there are only 2 wires to each indicator. LEDs do need to be wired with the correct polarity and have either an led flasher unit or resistors in line, but apart from that its a straight swap from the standard indicators.
Even though Britain is leaving the EU, it will still be part of Europe, and as such will still be subject to the emission laws covering Europe. Yamaha aren't going to remap bikes specifically for the British market.
Yamaha aren't gonna put a bike on the market that doesn't pass the current emission laws, so yes, nowts gonna happen.
If the bike is really that bad to the point of being uncontrollable, then maybe there is an actual issue with your particular bike, tps sensor alignment possibly?
No point in giving out to the bike shop mate, bugger all they can do about it, unless they have a dyno and reflash facilities. Nowts gonna cure the problem without removing the euro4 fueling bollix.