The AHK script I've yet to get to work but haven't devoted time enough to determine where the error is at (Mamewah, the AHK script, Johnny 5 setup, or my other .inis). As far as not asking questions or raising bug issues publicly, I have remained silent primarily due to my inability to formulate intelligent questions. 
AHK Troubleshooting - See
http://fe.donkeyfly.com/forum/index.php?topic=162.0 and the end of the Johnny5 WIP thread above.
If you are running Win98, that's probably your problem. I have had no luck with it in 98, but would like confirmation of others having problems, or anyone that might know of a solution.
Otherwise, like anything else, I recommend setting up a program in manual mode first and then automating things later. For example - First make sure you have the latest Johnny (or maybe the one or two day old one from the thread above.)
Open a command prompt and Navigate to the Johnny directory and run "Johnny5 1942 -clone 1942" - this verifies that Johnny5 works and is the call made in the script.
Now, I like to install the script in the same folder as Johnny, but it doesn't matter. Modify the AHK file to point to the folder where Johnny is installed and save it.
Open a command prompt and navigate to the script directory and type "J5 1942 1942". You should see the AHK "H" logo in the taskbar. Now press the P key. Johnny should come up. You have now verified that the script is working and Johnny is working. Hit P again and the script should stay loaded (until you press Escape).
Now navigate to your MAME folder and launch MAME. Press P and Johnny should come up after a short delay (it will show the controls for 1942, but that's expected). You have now verified that Johnny and MAME and the AHK script is working.
Okay, the above is as far as I have taken this, b/c my arcade computer currently uses 98, so the AHK script won't work, and my frontend currently can't really launch batch files, so there's not much point going further, but the next steps are: Create a file called mame.bat (parameters will be -gamename and -clone of).
The file should have the following commands:
call J5 %1 %2
Mame %1
exit
It may be necessary to add paths, such as:
C:\
cd\
cd johnny
call j5 %1 %2
cd\
cd mame
mame %1
exit
Now open a command prompt, navigate to the folder that contains mame.bat, and experiment with different games and clone of games, ie "mame 1942 1942" "mame gyrussce gyruss", etc. Verify MAME launches the correct game and johnny displays the correct labels.
Now you just have to modify your frontend to call mamebat followed by the gamename and parent name, rather than mame.exe.
Post back where you are getting hung up and we'll try to work you through it.