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Yes, the "engine" light is the MIL light. If you have never changed out the high pressure fuel filter, that can very likely be causing the problem you describe.
The VST is the vapor separator tank. It is located on the right side of your engine at the back where the upper cowling meets the engine cover. The VST is in place to assure an adequate amount of non-turbulent fuel is available to the high pressure fuel pump. (The fuel in the VST tank is kept underpressure to prevent vaporization, thus preventing the fuel from becoming too lean under variable demand.)
On the back starboard side of your motor, you will see a clear plastic tube looped around a holder. Unhook it, and look down at the base where it connects. Beside the connection is a small set screw. Use a long 10”or longer, flat blade screwdriver to open the set screw - slowly. With the end of the hose extended downward into a clear container that will hold at least a quart of liquid, start opening the set screw. Do not open too far - if it comes out, you will need to remove the cowling to retrieve it. Anywhere from two to three pints of gas, and maybe some water and gunk will come out of that tube. Be patient, the last stuff to come out is usually slow, but drain out as muchas you can. If there is water, or any gunk, then your fuel-water separator and low pressure fuel filter have failed and need to be replaced. At that point,you should also change out the high pressure filter which sits on top of the fuel pump and is held in place with three 5 mm screws. If there is no flow,blow low pressure compressed air back through the tube to open it up.
Before trying to drain the VST again, turn on the key switch for about 10 seconds to let the HP fuel pump charge the system, then try it. You may need to blow air back through it again.
Please describe the alarm again - are you saying that you are getting a single beep every three seconds? I think that the normal interval for the "long" malfunction beep is about 1 to 1.5 seconds.
Back to your original issue of the malfunction beeps. If that is a legitimate malfunction, then the EPROM in your ECM will be storing a fault code. Have you tried pulling the malfunction codes by shunting the service connector, as has been described many times on this forum. Alternatively, send me an e-mail at [email protected] and I will send you the procedure for pulling the codes.