When you say 'std. hole lower' do you mean a sm. pin or lg. pin lower?  The vast majority will be sm. pin upper receivers because that is what's most prevelant.  If you have a lg. pin lower you can use a conversion pin to mate a sm. pin upper to a lg. pin lower with little problem.  If you wanted one custom built with a lg. pin upper receiver you provide I'm sure the manufacturers can arrange that also.

There is no standard mag for the .40/10mm/.45 uppers, some are using Olympic Arms blocked Uzi mags, some use modified Sten mags and some use the Dalphon style converted M3 grease gun mags.  I haven't heard about the use of Thompson mags but I may have just missed it.

Sm. pin uppers will be what you find so don't worry abut that part.  Olympic and Dalphon are the two big names but recently Dalphon has had some sales problems so I'd cross them off.  

There is another member here who has started manufacturing pistol caliber uppers, Kurt's Kustom Firearms (user name - 'KurtsKustom'), you might want to talk with him about prices. He is also the one working on using Sten mags which are inexpensive.

There are a couple of members here who have sold O.A. conversion uppers on a somewhat regular basis, you might post a 'WTB' ad over in the Equip. Exchange to see what responses/prices you get.