I am actually about to do the same thing.
I have been running a redtop with a SC-12 bolted on - running on propane for a while but am switching to the gze shortly ... finally bought an import gze this week - got rooked - but I'm tired of waiting, and I am looking forward to see what I can do with an engine with lower compression and stronger pistons.
Anyway the things to look out for ...
did you just get an engine?
Then the hard part is wiring the new ecu - there are some diagrams nd DIY's on club 4ag that look useful.
If you are installing the new tranny too you will need to either buy - replace or build a new transmission mount and source the heavier axles and hubs.
Here is what I am going to do.
before installing the engine the mods
I bought and engine tranny combo but I am keeping my current tranny in just to make the swap easier.
1) get an upgraded clutch and flywheel I keep reading that HKS makes a good setup but I have yet to see an actual model number - I'll update if I fid it.
2) replace the fuel pump with something a bit bigger ( check the wreckers for a 7mg supra or cressida I haven't done this yet but my research tells me they should bolt in.)
3) My advice if you have the $$ put in a front mount I/C right away. I don't have the $$ so I am going to have to cut a hole in my existing hood to fit the intercooler or source. On my N/A engine I used a water to air setup - the intercooler from the celica 'just' fits between the engine and hood. I then went to the wreckers and got a pump and front mount rad out of an Audi. The setup did seem to get heat soaked under hard driving and the recovery rate is slower than an air/air but hey .. it fit.
4) Mount a larger (3 row deep) radiator I have come perilously close to overheating a few times - not good.
Next get the thing up and running smoothly
After the car is up and running the mods I am looking into will be
5) water injection - any time you can decrease detonation and increase power for less than 150 bucks ... its a good idea here is a how to
http://www.dawesdevices.com/howto.html - note see my wiring below. Not that it matters much buy I used this pressure switch...
http://www.dwyer-inst.com/htdocs/PRE...iesaps-avs.cfm
6) I will also be rewiring the S/C clutch so that I am in control of it in lieu of the ecu. I ran this setup on the N/A motor and it worked well this rewiring also included control of the H2O injection.
SC Wiring
7) A smaller S/C pulley
8) A front mount intercooler
9) Convert the thing to propane
10) Find a bigport head and have it ported and install ford focus 1.8L springs
11) Mount the new head and go turbo.
12) Source the tranny mount and heavier axles, and mount the E series tranny.
In truth at the rate I get things done I doubt I will get past (7) in the next year but if things go well or if I come into some extra cash I could be running propane again by spring.
( At least I hope so ... gas at the pump is now $1.07 here in calgary and propane can be had for less than 60 cents .. and less than 50 cents if you look hard enough.)