Welcome to the STD Forum. The exposure you describe carried virtually no risk for STD (including HIV) acquisition and the testing you have had since confirms that you did not become infected through the exposure you describe. Your vaginal exposure was condom protected and classical STDs are not transmitted by kissing. HSV-1 can be transmitted by kissing but in the absence of a lesion on your partner's lips, would be most unusual. Further, your symptoms are non-specific and the testing you have had is, when considered in context, definitive. To address your specific concerns:
1. If you had an initial outbreak of HSV-1, the lesions would have been more obvious and your tests would have probably become positive. that the cracks have come back several times does make one worry about HSV but if this is what is going on it is more likely that you had HSV-1 before and these are recurrences. Your negative blood tests make this less likely and suggest that something else, perhaps just dry lips, combined with anxiety, may be causing this. Recurrences of HSV almost never come and go in only 2 days. The only way to prove this is HSV-1 would be to have a positive culture or PCR test taken from the lesion and in the absence of that, I feel confident in saying this is not HSV.
2. Yes it would. As I said above, that they were both negative adds to the evidence, along with the atypical nature of the lesions, that this was NOT HSV.
3. There is some debate as to the best time for follow-up testing See Dr. Handsfield's recent comment to another client
http://www.medhelp.org/posts/STDs/HSV-Clarifications/show/1306350 ) but in the context of your situation, a 12 week test should be sufficient to completely rule out HSV.
4. All STDs, including HIV have now been ruled out.
Hope these comments are helpful to you. EWH