I know it's been posted about the suspension set-up and I HAVE read throught the posts on the forums also. I am however confused with aactuaal set-up.

First of all the info...
04' 1000RR
Lowering link in rear, and front triple moved down to match.
Front-NO lines showing on Preload, rebound 1 1/2 turn from full hard, comp 1 turn from full hard
Rear- NO idea on preload, rebound 2 turns from full hard, comp 2 turns from full hard, ( I THINK) set0up by someone else
Rider 6'0 220lbs

For conversation lets stick with the front setup. Being lowered for my size, should the preload have some lines of adjustment showing?? The trouble I'm having is that under braking, (normal), the front end dives somewhat too much I think, it has a lot of travel. as far as bumps and what not go so far it seems good.

I'm having trouble distinguishing the difference between toomuch/ too little adjustment in comp/rebound. What are the tell tale signs for each?? I'm not very mechanically inclined, but no idiot, I follow directions pretty well when I can understand them.

I wont be buying any Ohlins shocks for some time, so I have to make due with the factory set-up. I looking for a more agressive ride in the corners and greater stability/traction for my weight.

The reason the bike is lowered for such a big guy is I have a bunch of hardware in my knee from being hit on the freeway last year on my 600RR and the knee isn't quite 80% usable or flexible.

Thanks

 

You just summed up all your problems. From what I hear the 1000RR like to have its nose up in the air (dropping the forks will kill the way this bike handles)
For your weight with the stock suspension you need to raise the forks and crank the front preload to max , loose the lowering link and put the shock to med. soft.
If raising the bike is not a option I don't know what to tell you other than the forks are to soft and the shock is to stiff.