The shorter line is for the right caliper as it is closer to the master cylinder. I have aftermarket clip-ons, which are much lower than stock, so I had no problems with length on my Galfer lines.
You can raise the fork tubes in the triples as much as the stock bar will allow, it will make the bike steer quicker and help with you problem.
I never tie off the lever, just keep the master full while you pump/bleed the system. You will know when you really start pushing fluid as the master will deplete fluid quickly. Just make sure you keep it more than 1/4 full at all times. Rotate back and forth between front calipers several times and keep going until all air bubbles are gone.
Good Luck, Ed.
2005 GSF1200SZ
1983 GS750ED