A good ECU should be able to use the 4A-GE standard crank angle sensors, just with software configeration. I am not sure if the Haltech can use this or not. Just ask Haltech if it can use a stock Toyota magnetic pickup. Some ECUs can use the stock pickup, but need a tooth filed off, but I have avoided doing that.
If you want to change to a Hall effect sensor, then there is no use going to the 4A-GZE unit as it is exactly the same as the smallport 4A-GE as far as I know.