Bluetail-Back to your question!!!! My experience has been that it does take a little time for the muscles in the neck and possibly back to adjust to a road bike. If I have not done a longer ride for a while, I notice that my neck and related shoulder muscles are a little sore the next day. However, after working up to the distances I want to do with shorter rides, most of that goes away. It really doesn't matter if they are flat bars or hoods-probably what has changed has been the bars are now a little lower than the saddle and they are probably also a little further away. I've noticed it does feel a little stretched out at first but it is also easy to get acclimated to. As long as the bike is fitted within reason you should be able to adjust to it over time. You should be able to sit on your sit bones with your hands on the bars, you should also have some bend in your elbows so you're arms are not straight and rigid. If you're arms are straight the shock and bumps from the road will go directly to your shoulders and back-not good.

If it were me, I would do some slightly lesser shorter rides to get more acclimated to the new position, and then tweak the positions later depending on how things feel. It really does take a little time to work these things out.

Welcome here as well. Let us know how it goes.