no, the default lookup tables in the ecu will keep air/fuel ratio safe enough with the maf unplugged (assuming that is the only faulty part on the fuel side of things). 99.9% certain the crank sensor is causing your warm start issues. That shouldn't cause any damage since as soon as the ecu see's an implausible signal from the sensor it cuts the ignition. When they begin to fail they tend to start showing symptoms once the oil temp is above around 70 degrees.
I don't see why they limited your torque, a normal stage one map makes around 230ft/lb on the standard smic and cat back..
How have the managed to map a car with a faulty MAF surely air/fuel ratio would be completely wrong and it can't be something you can guess
Take it back I'm no expert but clearly something not right was the car scanned before the map