Well guys, here's the update on my bike...
Last saturday a friend of mine and myself lifted the rocker cover on my bike to replace the suspect intake seal. The intake seal, genuine from Yamaha only cost me $7.50 Aus.
We thought that we may have to drop the engine or remove the front engine mount bolts to tilt the engine forwards a bit to be able to get the rocker cover off, but it turned out that you can remove the rocker cover without touching the rest of the engine, which saved us a lot of time and hasstle.
We tried the rope down through the spark plug hole trick, but it didn't work too well. I think that all the rope was sitting down around the exhaust valves. We ended up just bringing the piston up to TDC to stop the valve from dropping in and using a couple of screwdrivers as levers to compress the valve spring. It all went relatively smoothly and was easier than expected. We were hoping to find that the seal was demolished or at least cracked, but it seemed to look okay. It was rather loose on the valve itself though and couldn't hold the valve in place (the valve would drop down onto the piston under its own weight). Once we took the seal off, there was evidence of oil having been underneath it, on the side of the seal that should be relatively dry. The valve guide felt good, with no excessive amount of lateral free-play, so we replaced the seal, re-fitted the valve springs and rocker cover, adjusted the valves and then re-assembled the rest of the bike. The initial startup upon re-assembly resulted in a small amount of smoke blowing, as I had expected. It's been started 5 times from cold and done about 50 km since being put back together and it seems now that each time i start it there's less and less oil burning happening. The last 2 starts have resulted in practically NO oil being visibly burnt. I'm guessing that over time any oil that is still hiding in the valve guide is slowly being burnt and any deposits on the valve are being washed away by fuel and the bike is starting to run clean again. Even on its first start, the smoke that came out was probably only one tenth of the amount that was coming out before the seal was replaced.
At this point in time it seems like my problem is solved, but I will be continually monitoring the bike incase things turn bad again.
Thanks for all your help, advice and suggestion on this topic.