Happy to see you made some progress. OK let's try things one at a time.
1- for the GPS module please make sure that it's connected correctly to the minipix as it's easy to get the connectors the wrong way around.
2- for accel calibration make sure that you have a level surface and there is no motion before you click next. If that doesn't work it might be best to try reset the board but loading arduplane onto it and then arducopter again. I have had something similar happen before and spent an entire afternoon trying to figure out what was wrong, but after a reset it was perfect. There are hundreds of parameters that you can change and sometimes if one of them are wrong it can mess things up, so best to start with a reset on your pixhawk.