I am getting a bit upset that we are giving you advice which you are not heeding. Either that, or there is too much advice and you are getting confused.
It seems to me that your knowledge is a little lacking, and you will have to, therefore take things step by step. You will insist in connecting everything up and switching on and hoping for the best. This is not a scientific way of doing it.
You had better give your computer the once over first and see if signals are still coming out of the LPY1 port. .
Is this a standard shop bought computer, or one you have put together yourself. Is the chassis earthed.
Connect a cable to the LPT1 port and turn on the computer. Do not connect anything else. If you have Mach 3 on the screen then fine. Has Mach 3 properly loaded onto your computer, with the drivers running. Have you run a driver test.
Do all this before going any further.With Mac 3 running check with a volt meter, or a logic probe, the signals coming out of your printer port. What voltage are they at. Check each wire 1 to 17 against one of the signal return wires 18 to 25. The pin numbers are stamped on the plug (somewhere).
What voltage is the sheathing showing
The sheathing should be at 0v and pins 18 to 25 should show 0v to each other and the sheathing. No other pin shoud have a voltage on it greater than 5 volts. If there is anything wrong - particularly stray voltage on the sheathing, FIND OUT WHERE IT IS COMING FROM before you do anything else.
Moving to your Bob board - it sounds like you have now bought one of the opto-isolated variety. WHY DO YOU INSIST ON CONNECTING 12 VOLTS FROM YOUR FAVOURITE VOLTAGE REGULATOR TO IT. This is a recipe for disaster. The opto isolated board - if it is from the same stable as your last board has a simple connector - a USB connector, which you plug into your computer and into the Bob board. This provides power to the Bob. Since it is from the computer, then all voltages must be the same.
If you LPT1 cable checks out, then plug it in, fasten up the USB link and the Bob should now work. I cannot percieve anything more simple than that. DO NOT CONNECT ANYTHING ELSE TO THE BOB UNTIL YOU HAVE TESTED IT.
That is enough diatribe - if you get that far (and live) and want some more, come back.