setting up a generator
&lt;disclaimer&gt; 
Unless you're an electrician or someone who has had some experience with electrical work and you're working on your own home, do not try to connect a generator yourself. You could endanger not only yourself, but also anyone that might be working on the mains. &lt;/disclaimer&gt;

Use a search engine and read up on "how to safely connect a generator". It's interesting stuff to read, but see the caveat above.

If you're considering doing this without a transfer switch or interlock, you should consider whether you would willingly put another person's life at risk. Notice that you yourself admittedly accidentally messed up the order. Imagine what might have happened if you were under stress and you forgot some other important step. 

Your generator may have lost one of the windings due to the error. I suggest you have it checked by someone who knows what they're doing with generators. That said, measure the voltage at each phase to neutral. 120VAC is nominal. Check out the TM, too. I found this reference that might get you started: http://www.steelsoldiers.com/showthread.php?146273-MEP-004A-No-output-after-starting (although I admit this points to the voltage regulator and you said you have none.) The TMs for the various models are here as of this writing:
http://igor.chudov.com/manuals/Military-Generators/MEP-004A/

Good luck. Hope you didn't fry something, but from where I sit it really sounds as if may have done that.