Jph1, if you're going to have your 9000ES modded, there's really no need to break it in before doing so--it'll need to break in again once the new parts are installed. I had the the full blown mods (about $1,900 worth) done to my unit by Dan Wright and I couldn't be happier. The audio is much improved in all three formats. The noise floor is incredibly low, allowing music to become much more involving.
You should contact Dan via his website to review the different level of mods he offers. He's very easy to deal with, but is quite busy at this time. As far as the time he will have the unit, he will work that out with you based on his work schedule. He'll get you on his list and let you know when to send the unit so that turn-around time is kept to a minimum.
My unit is absolutely amazing. My brother has a modified SA-14 AND an unmodified SCD-1 (which Dan will be working on soon), and he believes my 9000ES sounds as good or better than either one (and mine blows away his on DVD ;-)).
A few caveats: to fully realize the benefits of the 9000ES mods, you MUST have comparable quality equipment. Most importantly, you must have a very good preamp (I use a Placette Passive Linestage which is fantastic) as well as cables that don't get in the way of the music (I use Harmonic Tech cables exclusively). Finally, you need speakers that will truthfully reproduce the audio signal coming from the 9000ES (I use Spendor SP-1/2E's coupled with a pair of Velodyne ULD-15 Series II's).
My system is about as transparent as any I've heard, due in large part to the modded 9000. It sounds better as a stand-alone unit than when I was using my Classe' DAC-1 (which is a very nice DAC!).
I highly recommend that you have your 9000 modded by Dan. It'll give you the best of three worlds--all in one box.
Hope this helps. Scuba.