Hi mate, done this a few times so will help as much as i can.
I'm not sure about GTi box to be honest, dont know if mk4 shafts will fit it, plus the rear starter location could be a bit tricky. I'd advise using a mk4 box (any will fit but RST would be preferable as has LSD) as its a straight fit to zetec, and obviously original cradle, shafts, speedo drive and linkage can be used.
Rev counter is a bit harder, i'm still tryin to get mine to read correctly, if your using full GTI loom and management it might be a bit easier.
I run an XR3i radiator in mine with a bit of fettling to get hoses to fit neatly - its worth noting that the Zetec's run hotter than CVH's so dont worry too much if temp usually sits midway.
I run a 2.0 in mine below:
any pics of yours?