With the gears line up on stock bike which cylinder to install push rods.

Tom

 

don't worry about timing marks,get the cylinder on the compression stroke,get the lifters at their lowest point & adjust the p/rods.wait till they bleed down and do the same on the other cylinder

 

First photo is front cylinder at TDC and second is rear cylinder at TDC. Like Kirby says, make sure the piston is on the compression stroke and near TDC.