I am not really sure what to suggest for you...
Let me share my experience, you cant cheat your chart. No matter how good it might look with the adjusting and stuff, it does not make it real IYKWIM. (I have been know to try this out... )
I would just enter the temp taken after the most consistent period of sleep (did you get in 3 hrs and any stage before temping...) and make some notes to remind yourself what happened. I am a terrible sleeper, and I temp a couple of times in the night sometimes, and I just enter the one after 3 hrs sleep... seems to get a pattern for me. Did you use OPK's or another means of checking your O day. I find they help too in pinpointing O if I am having sleeping problems.
Good luck and hope you are feeling better soon.
xo