Im not sure about your cars particular sutiation, but I know that one alot of domestic cars when checking for basic trouble codes, without a scan tool, there are certain actions you can do such as turning the key to the on position without actually turning on the engine that will give you a code whch you can check from a list online or on a basic repair booklet. I dont own a miata so im not sure what the troubleshooting methods it requires to attain the trouble codes. Isnt there a booklet at an auto store you can purchase that may help?

You should also try disconnecting your battery cable to reset your PCM, maybe you accidentally moved a sensor or somthing when cleaning around the bay and it messed something up. try that and see if that works.