I do close to what jd does above. I scan with Vuescan, then go directly into Lightroom (sorry PC based here), then Photoshop for mostly touching up.
Rereading your post though, it's seems to me that you have your post processing methods down pretty well. Let me tell you lazy I am.....with RAW I strictly use Lightroom to adjust the basics and correct 90% of what needs to be corrected there, then use Photoshop to play with all the little bad things I want to get rid of. If I get lazy and shoot JPGs, then right to Photoshop I go. Being more lazy than not as of late, I got a Lightroom/Photoshop plug-in called Perfectly Clear at "automatically" adjusts color balance, contrast, blah, blah, blah. Well, for me, 99% of the time, what it does is good enough. So when using RAW in Lightroom, apply plugin, fine tune maybe, off to Photoshop for the end. JPGs.....open them in Photoshop, apply plug-in, then fix the bad parts and off to the printer we go.
So in a long way what I am trying to say is, if your getting the results you want and can live with moving this and that back and forth from Aperature to Photoshop and back again......your good to go. I would advise that unless you feel there is a noticable loss of photo quality you can see moving stuff around like you are, don't worry about it. If you can really control Photoshop as you are indicating you can......you have 99% of it made. You may be "over thinking" this.
Bob E.