Oldskool,
I'm glad you have tried something different with your old hardware; people settle for standard stuff too often when they can be improved cheaply.
Regarding the damper rod holes, probably best to start by reading this:
http://www.racetech.com/page/title/Emulators-How%20They%20Work(Racetech originally designed the cartridge-emulator valves). I have lifted what I think are the relevant parts below.
"
Compression damping is controlled by the number and size of the compression damping holes and the rebound damping hole(s) along with the oil viscosity.
This type of damping is referred to as orifice-style damping because the resistance is created by forcing oil through holes or orifices.
As long as the compression stroke is not too rapid, orifice damping can provide a reasonably comfortable ride as the front wheel hits small bumps. Unfortunately, not all bumps are rounded and small in size—when a square-edged or large bump is encountered, orifice damping can create a very harsh ride. Because oil is not compressible, the faster the fork compresses, the faster the oil is forced through the compression damping holes.
As long as the compression stroke is not too rapid, orifice damping can provide a reasonably comfortable ride as the front wheel hits small bumps. Unfortunately, not all bumps are rounded and small in size—when a square-edged or large bump is encountered, orifice damping can create a very harsh ride. Because oil is not compressible, the faster the fork compresses, the faster the oil is forced through the compression damping holes.
Perhaps you’ve considered increasing the compression damping hole size as the solution for the harshness problem.
The larger damping hole will be mushier, though it will be better at high speed. This style of damping seems to provide the worst of both worlds—harshness and bottoming.The Emulator takes over compression damping duties from the damping rod. To do this the damping rod compression holes are enlarged and, depending on the model, increased in number. With larger flow area the restriction at the compression holes becomes negligible. It is certainly still there, but the effect is so small it is no longer significant. Instead, all the compression damping takes place in the Emulator"
So, the emu takes over compression damping by controlling oil flow and this is achieved by killing off the original compression circuit. But you've asked a good question,
how much (if any) is enough to override the standard system? I can't give a definite answer but can only draw info from others, and the most popular usage of these types of emulators are the SV650 owners, whose forks are apparently even worse than ours. There are lots of opinions about the amount of holes and how much to enlarge them. Some claim that drilling holes is not necessary, others that enlarging the existing holes is enough, others saying you need extra holes.
Here is an example of the bunfight / gunfight regarding the drilling of holes:
http://www.svrider.com/forum/showthread.php?t=78075 Me? I'm going with the opinions of the emu inventors but you may want to start by keeping the damper rods in their original state.
From a structural point of view, the more holes (or larger the holes) you drill the weaker the damping rod becomes. I drilled six holes, which on hindsight was probably overkill and if I was doing it again I'd probably drill less holes. You could start with two 8mm holes at the bottom of the damper, but IMO that would be a minimum starting point. If it's not enough to you will still have some of the original harshness as the original compression circuit has not been over-ridden. This means you'll have to take it all apart again in order to modify the damping rods further...and then reassemble again!
This excellent article for converting the Suzuki Burgman
http://burgmanusa.com/bkb/650+Race+Tech+Installationlists several options for the number of drill holes and their diameter (Step 5 of his instructions). He went with a total of four 9mm holes but you could try other options such as two 10mm holes or four 8mm holes.
If someone out there understands flow-rate calculations then we might get a definitive answer, otherwise my advice would be to drill as few holes as you're comfortable with, as long as you accept that you may have to take it all apart again for any further modifications. I've Googled for damper rod failure as a result of emu conversions and can't find any hits, so I'm assuming if the drilling & hole spacing is done *correctly* it isn't an issue.