Just thought I'd post this up here as well as ASF in case it comes in handy to somebody...
With the fairings off the Minja after Woodsy munted them up taking it motocrossing on our recent trip to brisbane

I found the bike simply wouldn't run at freeway speeds. The engine would cut in and out and every gust of wind would cause very uncertain fuelling.
As I anticipate the bike will be like this for some time, I went searching for information to help me solve the problem. Turns out it's because of the float bowl pressurisation tubes no longer being equalised in pressure with the airbox once the ram air system is removed. A simple hack can sort this out nice and easily, so here's what I did:
For reference, this is on a 1994-1997 B model ZX9R:
The two bendy tubes coming from the carbs up and out through the frame holes to the front of the bike are the float bowl pressurisation tubes. Not sure if they're the same on a ZX6, I know the ZX7s are slightly different as are the later model E ZX9Rs. There'll be something though.

Using a $2 copper t-junction from bunnings, I've cut and joined the two float bowl pressurisaton tubes. I've then stuck another straight bit of cut-off tube so it points up through where the airbox will be. I left it long so I could cut it down when I knew how much it should poke out:

Re-fit the airbox and locate roughly where you'll need to drill it, then go for it. I tried to make the hole a bee's dick smaller than the tube diameter, to keep the airbox sealed. I failed. You might succeed. Please note scratch trail where ham-fisted drill user has lost control and wandered off down the airbox:

Drill the filter next - it's very flexy so you can make a fairly small hole. You definately want this bit to be airtight. Fit the airbox with the tube up through it, then fit the filter and poke the tube through. Cut off the excess length so the cover will fit back on, and voila, there you go. The bike should now run without any surging at high speeds - although the jetting will need some adjustment to match the new airbox behaviour.

Bob's yer uncle now, the Minja is running fine although a bit lean if I understand it correctly. At least it can do freeways now. It's also an easy hack to reverse if you want to put the ram air system back on, because all you do is re-route the hoses and plug the holes and you're off.
Further reading, relevant to all kawasakis, here:
http://www.factorypro.com/Prod_Pages/prodk51.htmlhttp://homepage.ntlworld.com/webzxr/zxr ... tbowl.htmlhttp://homepage.ntlworld.com/webzxr/zxr ... carbs.html