Yes - the ones on key-switch loom - the two you join are the Blue & the Red.
That was assuming removing the actual key-switch and salvaging the connector/harness to still utilize the OEM main harness interface.
Keyswitch -> Main Harness
White -> White/Blue
Brown -> Blue/Yellow
Yellow -> Green
White/Black -> Orange
White/Green -> Orange/Green (& Black/Blue)
Red -> Red/Orange
Blue -> Red/Blue
If connecting to the main harness, you can actually find all of those wires* at the Fuse Panel, where you can conveniently tap onto them at the rear of the bike, where it will be easier to mount the relays and control box.
* with exception of the Orange/Green - however you can also find that at the rear - either at the indicator relay behind right side cover, or at the rear brake switch input
Relay 1
30 - run wire to connect to White/Blue at Fuse 2 output; also connect the red wire from control box to this relay terminal
87 - run wires from this terminal to splice to the Green wire at Fuse 5 Input and to the Blue/Yellow wire at Fuse 9 Input (note that you must get the correct side of the Fuse for these two wires!!!)
86 - white wire from box as per latest drawing
85 - Ground
Relay 2
30 - run wire to splice to Orange wire at Fuse 4 Output;
87 - run wire from this terminal to splice to the Orange/Green wire at the Indicator Relay
86 - white wire from box as per latest drawing
85 - Ground
Jumper - Run a wire to splice between the Red/Orange wire at Fuse 10 to the Red/Blue at Fuse 8. Alternatively you can just remove the those two wires from the key-switch connector (main harness side) and just join them together.
A third option as I look again, would just be to extend the link between the 8 & 9 fuses over to the 10 fuse also (probably easier/cleaner!)
(Note I already show the jumper connected between the Red/Orange & Red/Blue)
Don't know if you have access to PosiTaps; those are perfect for tapping onto existing wires causing minimal invasion.
http://www.posi-lock.com/posiplug.html