Here is a conversation I've been having with a gentleman on this board who feels he may be a little rich I've given him some of the experiences I've had with tuning and it may help some other people on this board:
I think you're right. If it's a little "mushy" down low it may mean you're compensating for a little lean mid-range. THis what I did to make sure I had my mixture screws close to what they should be. THis may help you, at least it's worth a try just to see what the bike does.
Because of the super grim stock jetting(we've all been there) I had to fool around with my mixture screws as well.
At first I had it at 3 turns out like it says in the Clymer guide. THis was way too rich. When cold or just warming up, the bike ran great with lots of power, however as soon as it became full hot, down low was mushy as hell. I pulled the spark plugs and they were black and sooty as hell and you could smell that the bike was rich.
So what I did was turn in the screws 1/4 of a turn and let it sit idling full hot outside so it can get cooling. I blipped the throttle(under 1/8th of a turn occasionally then let it idle for around 30 secs to a minute. After a minute or idling I shut off the engine and pulled the plugs. Low and behold they weren't as black anymore, more of a dark brown. Still a little rich but getting better!
So I turned them in 1/8th of a turn then let the bike idle again with some blipping and just putting slight pressure on the throttle to bring rpm's up a bit while still running on the pilots for 5 secs then let idle for 30 secs to a minute. Then shut off and check the plugs. Getting better, still a little too brown. Throttle response down low was getting way better too.
Finally settled at 2 1/2 turns out now and it's very close to 100% maybe slightly rich but I'll find out more in the spring.
The theory behind this is you want the bike to spend enough time on the pilots so that the plugs will tell you what's going on when it's on the pilots. The beauty of this method is that the plugs don't lie. I tried the turn the screws in till the engine died method but for the life of me couldn't hear any change of rpm's or dying off, and I don't have fancy sensors and other shit. This plug method is fairly fast to do, especially if you're already close.
I found a symptom of it being rich is if you let the bike idle for 30 secs to a minute(same as a stoplight) and just try to take off and it's mushy or "missing" then it may be too rich. To find out, rev the bike a bit to get more air in there, then take off, if there is no missing or mushyness(due to slightly more air) then you know for sure.
In you're case, it may be worth it to at least know where your pilots should be when idling/using low rpm pilot cruise levels so when adjusting your mainjets you're not simultaniously fixing 2 problems at the same time.
For example, if you use either my method or your own to get the perfect(or close) idling and low rpm/throttle <4000 rpm, < 1/8th throttle performance, then you have a good basis for adjusting needle position/main jet. If you want to compensate with the pilots, that's fine, but you should know where you need to set them when you start fiddling with the needle position. If you leave the pilots in "rich compensation" mode and try to adjust the needle you may be giving yourself 2 headaches to deal with an it may make tuning that much harder.
Hope this helps for whatever it's worth....