I'm inclined to agree with XTorange's post. Especially if you have over filled your oil tank. The clue is in your assessment that it smokes for 2 -3 minutes. If it were valve stem seals you are more likely to find that it smokes really badly for about 20 seconds at most. Really just a big puff before clearing up. If you have overfilled on oil, crank case pressure will build and blow excessively back into the airbox. This is exacerbated by the common failing of the oil stop valve (ball and olive affair next to the oil filter) allowing excessive oil to pool in the crank case overnight rather than retaining it in the oil tank.
Check your oil tank level after parking up overnight before switching on the engine. If it shows to be low by comparison after running for a minute or two you will have an strong indication that this may well be the case.

well I think we are on to something here. Here is what I found this morning. First thing I did was pull the air box side cover off and yes I found oil resting on the edge of it. I then checked my oil level cold and it was 1/4 below the full line with the lid NOT screwed down but just resting on top of the threads. ( I was told this is how you check it and to not screw it down, is this correct?) Then I put the cover back on and fired it up. sure enough smokes like mad. I ran it for about 45 seconds or so as seen in the movie and about 60 seconds later I rececked the oil. It wasn't even hardly on the dip stick. So I started it up and let it run for a minute and now it's reading like it's way over filled. I tend to believe it may be as I just did and oil change for the first time and it took 3.75 quarts of oil with a filter change to read correctly or what I thought was correctly. So I'm thinking it''s overfilled but I don't know why it's sucking the oil tank down and taking so long to replennish it? How much oil should it take with the crank case drained and the oil tank emptied. I thought it was 3.3 liters which should be what 3.5-3.6 quarts? Any help is greatly appreciated as I just bought the bike and am learning about it. I know the air box is filthy so I'll clean that today but notice how it ran for a bit before it started smoking too.

picture of the oil
ImageShack - Hosting :: 1004412dl9.jpg

Video of start up.
http://www.youtube.com/v/JGtAQLGjsPM

I believe 3.3 litre is way too much.

The manual states approximate levels as such..

periodic oil change ... 2000cc / 2.1 US qt
with filter change ... 2100cc / 2.2 US qt
Engine rebuild ... 2400cc / 2.5 US qt

To check the oil level is a debacle in itself. Here is verbatim what the manual states:

1) If the engine is cold start it and let it reach normal operting temperature. Usually 10- 15 minutes of stop and go riding is sufficient
2)Allow the engine to idle for more than 10 seconds and switch off.
3)stop the engine and allow the oil to settle for 1 - 2 minutes
4)park the bike on level ground and hold upright.
5)Remove and clean the oil dipstick
6)reinsert it onto the threads in the hole, do not screw it in
7)check reading


if adding oil repeat above... etc etc


Hope this helps. DO DOUBLE CHECK OIL QUANTITY I HAVE STATED. From your video it looks like the 89 release model and not the 90 as you said. My figures are for the 89 model here....Yamaha XT 600