FB,
Glad you're finally getting a handle on things, but you are far far from break-in. To be honest I can't even think about how bad it could get breaking in a complete system, or at the very least, in my opinion, the two main components in a system, amp/speakers, at the same time. I listen to brand new speakers all the time, but always on well seasoned gear.
The tweeter does sound like your trying to force cookie dough out of it for the first 100-200 hours, the Mundorf cap seems real dark for the first 100 or so hours. Right from the get go, and even though the Mundorf's sound a bit dark, I think the realization for me, that there is no glare which seems to make top end to be more prominent and always wanting to attenuate the tweeter. Some pieces of music that I had previously thought were just poorly recorded, or that the mics had been overloaded during the recording process are as smooth as silk.
Now onto your room....When I built my room, and it was pretty much purpose built for audio, yet at the same time, I've aways had a desk in the right rear corner. At first it was just a typical desk, then transforming into an armoire desk with a flip down writing surface. A few weeks ago the wife and I did some room re-arranging and out went the Armoire, which means my room is totally audio. Back in February, Chris K from the forum had come down for a few days and he thought that my room was one of the best imaging rooms he had ever been in. This weekend, I flip flopped the room and everything from imaging to bass response has gotten so much better, its just like a changed my whole system. The side walls haven't changed, as it has Decware diffusers down both walls. The only thing that has really changed is that the live end of the room (no treatment what so ever) is now behind the speakers and the rear wall is diffused and bass trapped. Has me wondering why I didn't try this 4-1/2 years ago?
So give the whole system a good chance to break in, then start adding other components until you are in audio bliss!
I wouldn't worry about what other people say is the best way to set up a set of speakers. Like Lon said we all live in different rooms with different gear. What ever you like, is the best way to set up your system, period!!! I sometimes have to laugh at reviews, they show this list of some of the most expensive gear that they used for the review, then show a picture of the set up, which could probably be the worst sounding room in existence, and they are reviewing a piece of audio gear. Then I read where one speaker manufacturer wont allow anyone to review his speakers, unless they go to his place to review them. He also won't show his speakers at audio fest and the like because he knows how bad some of these rooms can sound. At the same time, he can diss a simular pair of speakers that he heard at one of these fests, without the disclaimer that the room could have had something to do with wat he had heard. Then argue it to the n'th degree.
Well enough ranting from me. Back to getting Steve's beautiful SE34-I amps bases

There is something about the dimensions and the gauges on this amp that are just so right...Hard to explain, its just right!
Zygi