I don't know about the Chicago area but Audio Classics in New York has a good reputation for refurbishing Mcintosh gear. Try them at www.audioclassics.com.
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One channel not coming up when cold is not an alignment issue!
The first thing I would do would be to test the tubes in the multiplex section to see if any are weak or shorted.
Alignment will affect stereo separation, alignment of the discriminator will affect distortion and where the middle of the signal seems to be, alignment of the IF section will affect gain mostly, alignment of the front end also affects gain and where stations show up on the dial.
If this unit has not been refurbished recently it would be a good idea to replace the filter capacitors in the power supply.