To my knowledge, factory.

In your case with the factory manual, I'd say the easiest way would be to reroute the starter solenoid power line (connects to the solenoid with a spade type connector)and run it to the g/box neutral switch, run the other connection back over to the starter solenoid - make sure the connector has insulation around it.
I would think the solenoid current flow wouldn't worry the neutral switch.
The starter motor is nearby, so your wire runs won't be too long.

The ECU won't now know if the g/box is in gear or not, but I doubt this will give any probs - can only run it like that and see over time. At worst, you may need to add a shorting link between pins 30 & 46 in case you have idle problems.
Unfortunately, I doubt the wires in Mark's setup shown above will be there, by virtue of the setup with uninhibited starts with the manual box.

I have done the remote start cicruit that EBGizmo wrote a while back, so I am hoping to integrate that onto the boot line using a relay, so nothing at all happens. Is this possible? Thankyou very much for your help.

NP.
What I described above will stop remote start in gear, but if IIRC EB_Gizmo's setup monitors the alternator light, so that means although the car won't start, the circuit may continuously keep power to the starter relay, as the alterator light won't go out.
It'd be best to reexamine his circuit, and figure out the best way to do it - an option may be to add a relay as you 've said to run off the neutral switch, to cut power from the remote start.