FWIW the throttle cables go over the brake line. Just changing the brake lines should not have caused an issue with the throttle cables so re-check your routing, making sure there is some slack in the cables and that they are not bound up by the brake lines. John (sailor) should chime in soon with his thoughts as he can interpret the GS-911 faults better than I can.
John is right about Sailor and interpreting the GS911 output. I do have a question. Did you unplug any of the cables on the left side around the throttle body? The idle regulator is likely the TVA and with the faults reporting as still present, Something is currently wrong. There is also a switch inside the TVA so that might account for the second fault. I would check the TVA plug to make sure it is seated properly. They don't go bad very often but there are a few reports of some failing. Your bike should start with no hand on the throttle if all is working properly.
In my opinion, John and Gordon are both correct in their message above... AND it also shows that these SPECIFICS GS911 faults (and engine behavior you saw) can have multiple "potential" causes.
FIRST... ALL THESE GS911 faults are both related to TVA (idle Actuator) and in this case I suspect it is only the messenger (symptoms) to something else - I doubt VERY MUCH the TVA is defective. These TVA are quite reliable and it would a fluke that is broke just after your recent maintenance.
These problems are VERY difficult to troubleshoot AT A DISTANCE without seeing the bike and using measurements tools (including GS911, Voltmeter...).
Let me explain further what I think are the 4 potential causes:
(1) While working on recent maintenance, you unplugged the TVA connector (or failed to seat the connector fully in). This would cause fault 5381.
(2) While working on recent maintenance, you remove OR loosen the 3 Torx screw holding the TVA , BUT later failed to seat/tighten the TVA completely flat onto its bracket. This can cause fault 1285 as the EFI system is expecting a direct response increase of TPS (measured in thottle opening degree) if TVA is able to push correctly onto the TB assy when needed (TVA will help maintain correct idle RPM in ALL conditions warm or cold).
(3) IF the free play in the main "pulling" throttle cable is incorrect, when the throttle is closed ,manually or with help of throttle-bodies (TB) springs, the butterflies of TB do not close completely (to normal idle stop). This confuses the EFI system as the TPS (Throttle-Position-sensor at end of TB) is expecting a specific very tight range of values at idle stop. When ignition is turned ON, just before start, the EFI system needs the TPS and TB to be at idle stop range.
(4) The TPS position (rotation) has been upset / moved either on purpose of accidently. Unless both TORX screws holding the TPS were loose (not common) it is very difficult to change the TPS position accidentely. I am including this as the LAST and LEAST possible cause, so we really need to make sure all previous items are correct before we go into this one.
To check item (3) or (4) above, you can use the "TPS check-adjust" routine screens in GS911. Their multi screens procedure is not very friendly (even confusing), AND you need to unscrew the TVA during certain part of the procedure. The reason for all this is the fact the base TPS setting needs to be checked when the TVA (idle actuator) is NOT pushing/holding in Throttle-bodies in fast-idle mode.
ANOTHER METHOD: To check TPS base setting (and if cable are holding TB opened), you can also use the "voltmeter method", but since you have a GS911, it is NOT normally required to use this alternate method. See attached PDF document...