Here is a link to a youtube video. I am not sure how to post the actual video.
http://youtu.be/Ru6fflAVaRw
The older Whipple SC uses a gear driven system located inside the snout of the blower were the oil reservoir is. What you are most likely hearing is gear lash from the blower. However if the sound is present on idle but not any other time then you have the "normal" sounds of the older Whipple CTSC. If the sound is there either all the time or only when the engine is either accelerating or decelerating then it is something different.
The noise only on idle is the most common and what most consider normal with the older Whipple CTSC, the blower uses straight cut gears and with time the amount of lash between the gears increases as they wear. The gears are not adjustable.
What is happening is every time a spark plug is fired the engine accelerates and every time the piston compresses the air and fuel the engine decelerates. These events cause the blower to speed up then slow down, this causes the gears in the blower to lash from the leading edge to the trailing edge of the gear making the noise. If you change to a light weight flywheel and clutch assembly the noise will increase and will be heard over a slightly larger RPM range. You can try different weight oils or additives to the oil to try and decrease the sound but making sure the oil level is full is a good place to start. Depending on the engine management you are using you can try and raise your idle. The higher your idle the less the effect of each ignition event will have on the blower gears and it will quiet or eliminate the noise. My car had little to no noise if the idle was set to 900-950 RPM, anything under that or when a load was added to the car (turn on the AC) at idle the noise would be there.
If the noise is there all the time you have an issue with the blower or an idler pulley, the idler pulleys are mounted on the front mounting plate and is used to route the belt from the blower to the crank. The noise from these can come and go but they are usually a higher pitch and can be heard from under the engine hatch and are easy to tell as the noise is away from the blower itself. You can do a search here on Prime there are many threads with locations and part numbers to buy the idlers.
If the noise is in the blower, it is most likely a bearing internal to the blower and cannot be serviced with out the proper tools and knowledge of how to disassemble the blower itself. You can remove the blower from the intake and ship it out for rebuild or repair if you do not have a blower shop in your area.
Most of the info here is common to twin screw blowers and will apply to other brands, but a lot of manufacturers have gone to helical cut gears to reduce or eliminate the gear lash sounds. I do not believe the Whipple design allows for a change in gear design but it may be worth asking if you having one rebuilt. Helical gears generate more heat and have more parasitic loss. They also can cause end play issues if the shafts being driven by the gears are not designed to used with helical gear sets.
Dave