strguy11,
I'm not trying to scare you or anything I would probably be doing the same thing you are doing, but just remember to look ahead and make sure whatever actions you take (writing or for that matter not writing something on the drawings, etc.) are not going to add undue risk to you or your organization. Like they say everything is okay until its not okay and then everyone starts pointing fingers.
For instance your Shop Drawing Stamp probably says something like Reviewed for Impact on Structure Only, etc., etc. Now if the dimensions of the embedments are noted on the drawings and they are wrong and you said nothing it could be construed that you reviewed them and since they do have an impact on the structure you may have some liability issues. Now suppose you corrected them and the contractor took note of them and it turns out the corrected dimensions are wrong and nobody else picked up on it, again you have some liability issues.
In each case most of the time on most projects things are handled as they say "Like Gentlemen" however, when something goes wrong its everyman (or woman) for themselves.
Since it appears that you have a little bit of a "rogue" or a "cowboy" contractor it is best to look ahead and Cover Your A$$.
Now if you let them get away with not providing the shop drawings or info requested in the Contact Documents you may also have some liability issues since you did not enforce the contract and may have not exercised your due diligence to the owner. In that case I would issue some kind of memo stating that the drawings are a required part of the contract and by not providing them the contractor is proceeding at his own risk and the owner should determine if they wish to enforce that part of the contract.
I'm not a lawyer, however, but I have worked for a GC/CM, a large Subcontractor, as well as Design Firms and have learned a little from each and now I work for myself (in theory at least, you still work for someone which is your clients) and I have also never been in a bad situation (luckily), but, what I learned from the GC/CM end is to be careful with documentation (or lack of) and how you state things in correspondence can be construed should things go awry.
Good Luck...
Also I have done my fair share of Steel Shop and Rebar Placing Drawings and They can be a pain in the a$$, but, I would recommend every engineer to do a few it makes you a better engineer. I wish I could say the same for some contractors (that is they should do some engineering it might make them better contractors or maybe just give them a headache).