Well-intended comments on this site by design emanate from, or are filtered through, the posters' past individual experiences. That is why the comments are so valuable when they fit your situation. The comments may, however, not exactly fit your situation. That is why you take what you need and feel is appropriate for you, and leave the rest. I am not saying that you should just ignore some comments, but I do suggest that you might modify those comments to fit your situation more appropriately as to DEFCON level or tone.
Reviewing your situation as you have reported, I perceive:
Positives
1. Your wife confessed to an EA "out of the blue". What was her reason to confess "out of the blue"? Was it pure guilt, or was she trying to disclose/minimize/damage control for self-protection?
2. The highest escalation of physical contact your wife said happened was holding hands. Hopefully, this prevented a "deal buster" event which can not be forgiven and disqualifies her for reconciliation. However, the possibility of minimization and self-protection is obvious.
3. She and he agreed to delete each other from their phones (albeit after the false NC).
4. After returning from friend's, she agreed to NC, job hunt, provide you access to phone, provided more indication of her culpability, expressed desire to reconcile
5. Her IC told her no contact was the appropriate solution
6. She said she couldn't believe she blew a twelve year relationship over two months of will they won't they sexual tension.
7. She volunteered to take a polygraph
8. Obviously disappointed that more messages weren't recovered. Poly is still on
9. IC said the text and poly requests were totally reasonable. She is accepting full responsibility and not shifting any blame to you. She is currently extremely cooperative. The reason she gave for agreeing to divorce temporarily was that she felt completely worthless as a person and that she didn't want to drag you down any longer.
10. She is at least seemingly committed to being completely honest about her emotions. She chose honesty over rug sweeping.
Negatives
1. Your wife had an EA (at least). Confirmation of no PA is critical. The unavailability of texts does not help. It is imperative that you resolve this with the polygraph as soon as possible. Confirmation will let out most of the tension in the situation and clear the air for reconciliation (after the issue of her feelings for OM are resolved also).
2. 1000 texts after an ersatz (and disingenuous?) NC promise with respect to "romantic entanglements" only
3. She lied and stayed out late with OM (Note that HE invited her to stay the night. That is a confirmed instance where he initiated. So that blows up the the premise that he always rejected her advances. Why then was the the reason to protect him after OBS confrontation?)
4. She enjoyed the sexual tension. She needs to resolve this issue through IC. The result would hopefully be a full understanding of her whys and her development of boundaries and capability to assure you that she can maintain those boundaries.
5. Blow back after your contract with OBS revealed and attempt at blameshifting. This seems to be proof that NC was broken, or not even implemented at all. Or, did OBS contact her directly? How did OBS hurt her?
6. She was clearly falling in love with him.
7. You indicated that there is are possibilities that you are being trickle-truthed and they have taken the affair underground. Do you still think that may be the case?
8. Both reading Not Just Friends and she read How to Help Your Spouse Heal from Your Affair. Have you had any discussions about reactions to content? Any thoughts after resulting actions?
9. No STD test. If there is no reason to suspect a problem, getting this done provides positive inertia and eliminates fear. It does not however guarantee no PA.
10. She still has feelings for OM. It would be helpful to posters for you to describe the level of her feelings. Did she actually fall in love with him? Is she still "in love" with him? Has she told you that she both "loves" and "is in love" with you? Why does she now decide for you? Are you Plan B? How will she prevent herself from reacting similarly when her next crisis develops and she must decide who to go to for comfort and support?
11. She would have gone, seems like the whole way. WORST negative - even if not consummated, intent is certain. Though IC she must fix herself on this so that this can NEVER happen again. She must absolutely, positively, genuinely commit 100% to you, forsaking all others, and find a way to convince you. You will still be taking a chance on her if you offer reconciliation, but you need to know that the risk could really be worth it.
Other questions/issues
1. During confessions, confrontations, discussions, everyday contact, etc. what has been her attitude, tone, demeanor? Was it matter of fact, or was she crying, begging for forgiveness, etc. Have there been any changes in her demeanor over time? It would be helpful to all posters for you to provide more information about the tone, flavor, and her posture and attitude during all of the confrontations and discussions. This information will help the posters to taylor their comments to your specific situation. Otherwise, the posters have to fill in those details from their own experiences (which might be dissimilar in extent to your situation) and therefore include bias.
2. Have you had your scheduled couples counseling? Posters have suggested (properly) that MC be deferred until after IC for both you and she have laid an appropriate foundation. But, if so, were there any developments during the session or after as a result?
3. Are you still on "D track" since you have not yet resolved the text messages issue?
4. How did she act on your trip? Any developments?
5. Have you scheduled the polygraph? IMHO, this is really a must-do, asap.
6. Any developments on the job hunt?
Again, the more information that you provide, the more relevant comments/advice you will receive. There is no reason to hold back on disclosures as an anonymous poster. Since most readers and posters have been in your shoes, they understand grief, shame, reluctance, shyness, etc.
Given all of the above, I see (with as much of my bias suppressed as possible) that a DEFCON 5 approach is not appropriate. I do think, as I have commented before, that you should demonstrate convincingly strength and the determination to get out of infidelity as soon as possible. Unless the affair as gone underground, she has been dumped by OM. There still is a possibility that she has implemented a strategy of "cake eating" or one of "settle for Plan B". You must figure this out during your recovery, and on into the reconciliation process. Hopefully, her sincerity, as shown through words and ACTIONS will reveal her truthfulness to your satisfaction soon. She knows that divorce is a possibility and that she is now competing for reconciliation. You might tell her that since she still has feelings for OM which cause you severe pain, that you must start the divorce process in order to protect yourself. You can tell her that you hope that the process will be stopped when reconciliation starts, but the pre-conditions for that have been discussed. I think the intent is to make sure that she feels that real consequences are in play for her and that you are not bluffing. You are not trying to force her to make any decisions (those must be made by her on her own) or trying to punish or manipulate her. You are only doing what is reasonable to protect yourself from critical damage due to a situation that SHE is 100% responsible for creating. If more negatives develop, you can always raise the DEFCON level as you need. You will continue to get excellent input from SI posters throughout your process, whether you end up with R or D.
I am still hoping for the best for you.