Either way it's a gamble now. Compromised head or compromised HG either way if it fails you're going to have to redo the job. I'd also be disinclined to reuse those bolts in the future whether they measure to spec or not. Loosening the fasteners that much is sure to compromise the HG's seal.
Myself, I'd redo the job but then I can get through it quickly. You can try and just ride it out a few people have done so without issue... and some have the head crack on them the head. Your odds are still better than those who toss a MHG on an unmachined block (although that's not saying much as that fails 90% of the time and you've probably got better than a 50/50 shot of things working out fine). You're not going to lose much if you try to ride it out and you can get a replacement head from a GE for little money; You'll need to re-shim the lifters when you swap over the intake cam but you should do those on both sides anyway.
Did you use moly when installing the bolts? Did you chase the threads in the block as directed? If you answer no to either of these well you may be in good shape but in bad shape for another reason.
Why don't people read the manual? These aren't made of Legos and nothing close to as simple as hanging drywall.
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