Indeed, I couldn't remember if the hoses were equal or slightly different lengths, thanks for clarifying that.
Regardless, it's a fuel-injected bike, you will sadly have to deal with the computer portion of the bike if you want it to run right. It's not hard to use Tune ECU; ask lots of questions here, some people have made video tutorials on it to make it easier.
Leave the secondary throttle motor connected, it doesn't matter if you've removed the plates. The bike throws a code if you unplug it without disabling it in the computer first.
Getting the list of engine codes would be ideal, but don't be too concerned with the engine light being on, if the battery was unplugged the light will remain on for the first three heat cycles if I remember correctly, and then turn off on its own. If it runs right after you've reconnected the hoses, MAP sensor, and replaced the plugs, ride it and enjoy