I'm late to the ball game here but I will throw tis out there for others or you if you find you need longer lines. And honestly, I am very surprised you got stock lines and cables to work with 12" apes. I wouldn't even consider that myself but you made it work. I would love to see how you routed all the lines with these new apes? Have you checked for tightness of lines and cables going from stop to stop with the engine running? Checked to see if it is disengaging your clutch any? What is the fender mod you are talking about. Anyway, back to the brakes.
As a dirt bike racer I have a boat load of hours bleeding brakes on mine, my son's and friends bikes. I normally try do this when I am not in a hurry and don't need to ride. I will unbolt the complete brake assy as one piece. I mean it comes off in one piece from the master cylinder to the caliper. Then I will remove the master cylinder lid and hang it from the wall, ceiling or whatever is tall enough. It doesn't have to be straight up and down at the master cylinder, just enough to keep bubbles going up the hose.
If I am changing out components, rebuilding the master cylinder (MC) or caliper or just have a stubborn one that won't bleed I will back flush the brake system from the caliper port up, this will make a mess so I usually have a bucket below to catch the mess coming out of the master cylinder.
A word about that bleeder port, put some heavy grease around the bleeder fitting. They are tapered threads and don't seal well when loosened. The grease will stop air from getting sucked in when you are back bleeding. Keep pushing fluid thru until you aren't getting much air. Level the master cylinder and push enough fluid so it fills up with brake fluid. Replace the rubber gasket and lid. If the rubber gasket extended when the MC got low push it back into place. Make the MC the highest piece again.
Let it hang for a few hours, I prefer over night, to let the air rise to the highest place, the master cylinder. I also tap the caliper, line and MC starting at the bottom working my way up to help any air move. I will do this a few times and it seems to help.
The rest others have covered but these steps have made my life a lot easier.