sredish, from what I have learned from playing with the dyno, it is safer to leave a couple hp on the table to be on the safe side of jetting. You will get the most hp from running right on the very edge of being too lean which is Ok for someone setting their bike up just for a few passes down the dragstrip. But I think this is a little to lean for someone that wants to go out riding for the day. So my answer to your question--
"Like, if I lean my main 1 size or even 2 and gain hp over the base reading, does the more power tell me it's right on or will I then have to double check that I don't have it too lean?
Would be yes you do need to make sure you aren't too lean. I have heard alot of guys say their bike ran the fastest right before it blew up.
I'm certainly not a know it all in the jetting department, just my .02 hope it helps you out.