I will try changing speaker locations and testing again. I'm kind of glad there was no optimizer mic included with the Yamaha receiver, because it allowed me to learn the skills to tune on my own by sound. The problem I am facing is that the system is too powerful to be put directly in front of me, that's why it's off to the side. I like to listen pretty loud, so I can't have the speakers pointing directly at me. Which means normal speaker placement is kind of out of the picture. I can turn the speakers around, and that helps a little bit but I will experiment more in the next few days.
As for the speaker upgrades, yes, I will be following your advice and adding two more RM 62 IIs. I got a really good deal for the first one at $200 and now they are going for $250 and up, but it's a really high quality mid range speaker, so it's worth the investment. Not to mention the fact that the real RMS is probably double what they advertise. Or at least that's what people are saying about them.
Also pondering the idea of getting a dedicated amp for my center speaker just to put a little more thumpity thump into the sound stream, and take a load off the A/V receiver.
For the record I have *already* partially destroyed (lol) two of the logitech speakers. I had to turn the levels on those two down (just a little bit, they still work fine), so I am using them as rear surround and the two good ones for the front. For the moment.