No you can leave it in for sure. You ll need to take off most of the centre console, bottom portion of the heater box under the centre of the dash as there are 2 nuts under there either 10mm or 13mm iirc. Also bend the heat shield out of the way in the centre exhaust tunnel. Removing the air intake will make this a lot easier to get to the top of the trans. and also to the heatshield.
Hope that helps, timewise I can do it at the wrecker in about 30 mins but thats with cutting and breaking things.
2000 ZX3 Open 2WD Rally Car