I usually do the sweeps between 3 and 4 am when it is quietest, park the car in the garage, let my heart rate drop down to 50, and hold my breath....
j/k
That used to be what you had to do with Alpine Imprint to get a good calibration, but not with the MS-8. Just make sure there aren't any loud noises inside the car during the sweeps. I like to wait about 30 sec to 1 minute after I shut the door before I start the sweeps, just to make sure all the electrical "gremlins" have had their moment. The head unit can (and should) remain OFF during the sweeps.
Why don't you buy the center from BSW if all the other speakers are from them? Whatever you do, make sure you include a tweeter in your plans! How are you going to drive the center?
Regarding inputs, seems you messed up the AUX input circuitry. I have not tried running the iPod directly to the MS-8, I'll have to try. In my case, it sounds crisp and clear using the speaker level outputs from the L7 amp right now. Soon, I will recode the HU to Hifi and feed the MS-8 a balanced low-level signal for (hopefully) even better sound.