Good to hear you got to the bottom of this.
If the gears wont select at the gearbox with cables disconnected it suggests something is wrong inside the box - this could be the cause of the timing being out.
Options are:
Rebuild current box - but likely you will need replacement parts and rebuild cost is expensive, but you get peace of mind.
Swap out for a good used one - lots out there, recently Pudding swapped his out for a Mk6 box, iirc he said the box was £260 reports better ratios and improved gear selection and they tend to have lower mileage than Mk5's
