A base Emerald map for a Zetec should get you reasonably close, so the issue you are describing makes me think something else is wrong. Here are a few things to check:
Is the TPS calibrated and operating correctly? Easiest way to check the latter is to hookup the laptop, go into the Live View and see if the Load Site starts at 0 and progresses to 15 as you move to full throttle. The engine doesn’t need to be running for this check.
Do the settings in the Injection Scaling window match the injectors and the fuel pressure you are running? If these are incorrect, then the entire fueling map will be off by some factor.
Have you reloaded the base map? Can't hurt to start from scratch in case something was corrupted when fiddling around earlier. Also, there are some other Emerald Zetec maps located here that you may want to check out.
When you write that AFR indicates the engine is lean, what are the readings? Are you data logging so you have accurate information with regard to load and speed sites, or is this based on watching the AFR gauge? If you aren’t data logging, then I recommend you do so. The Emerald will record up to 8 channels and looking at the data can really help you understand what is going on. I find the following 6 bits of data are the most useful: AFR, Load Site, Throttle Position %, Coolant Temp, Inj Duration, and RPM.
-John