I just finished my honeymoon period (pretty sure) It lasted me 8-9 months.
The first thing i did notice was my basal need went up, i went from 10 Lantus, to 12 Lantus every day. But the biggest thing i noticed was my bolus need pretty much doubled.
There was times in my honeymoon when i was adjusting my basal, at one point i was taking 13 lantus, but my carb ratio stayed the same. So i would say that the true indicator that your honeymoon is really over is that you need more bolus.
Waking up with high sugars could be due to many things. You could be eating low GI foods in the evenings so when you check before bed they havent fully digested and you get a normal reading and then in the middle of the night they raise your sugars, making you wake up higher then normal (I am bad with this and peanut butter... If i eat PB within 3 hours of bed its not fully digested when i do my last check )
Also, it could be stress raising your sugars, could be dawn phenomena, could be changes in the weather, or your fitness routine, an increase in basal need could be because you gains some weight (fat or muscle) and now just plain require more basal insulin. If you have a cold, or infection or something that would increase your insulin requirements as well.
You should try and check your basal ratio by waking up, check your sugars, and then fast for 4 hours (nothing but water, nothing physical) and check your sugars at the 2 hour mark and again at the 4 hour mark and see if they have gone up or down. This should tell you if it was something you ate, or DP or whats going on... Or at least help.