From what you describe it's like you can't find the gates, so it sounds like you need to adjust your selector mechanism. You'll have a gearbox with the rods rather than the cables.
There are a bunch of nuts on the selector mechanism on the gearbox, you just tighten or loosen them accordingly. It's either an 8mm or 10mm socket I can't remember which.
EDIT:
What you said about the clutch makes me think. Is it acutally the gates you are having trouble finding or is it just hard to engage the gear.
With the clutch not fully depressed (even though your pedal is) you will be trying to engage and disengage a loaded synchro ring. Which will massively increase the shift force required.