Do you write letters in the old-fashioned snail mail way? If not, maybe consider sending her little love notes every so often. She's caught up in NRE, but it won't last for ever. Hang in there! She has been with (waited for?) you for 13 years. That suggests there is a depth to her feelings for you. You just need to do a few things to stoke the fire as it were. A flame won't burn forever without some care and attention.
Apologise and explain why you said what you said. Reassure her that you love her very much, and then just let her have some time to process it all in her own way. I have faith that things will improve for you in the future.