With the clutch pedal NOT depressed the pressure plate is DEFINATELY engaged. The clutch/plate/flywheel should be locked up as one. Not sure what you are thinking might be a problem here, but the throw out bearing should be OFF the PP fingers/levers with the pedal fully UP. MAKE SURE this is the case! You do not want the bearing constantly turning!!!

As far as the rods, I know your supposed to insert a 1/4" Rod (drill bit) in the line-up hole on the shifter and then adjust the rods to fit but that didn't entirely work on my car. I ended up positioning the tranny levers in each gear (rods disconnected) then positioning the shifter in the appropriate gear and adjusting to suit.
Another way of doing this is go ahead with the 1/4" Rod method, then put the shifter into a gear, and then disco the rod at the tranny and check the tranny lever to ensure its exactly in position. On my car one gear needed a different adjustment than the 1/4" Rod method indicated.