It's really hard to say what will be safe to run, but definitely NA should be safer than boosted. I would still want HP Tuners to log data or at least the AFR gauge to try and have some idea what the fueling is doing. But you also need to think about what happens with the MAF sensor with the turbo out of the loop and probably lot of other details.
If this was me, I would probably go back and set the car up completely as NA by pulling the turbo, putting an NA intake and exhaust in place and flashing ECM back to stock. Then learn to tune the NA version with HP Tuners. Once you are comfortable tuning NA, then re-install the turbo. Or find someone that can remotely tune the turbo setup. I'm uncomfortable with the idea of trying to make this run without a better idea of what is going on with the baseline of fueling and spark.