Well, this is not "expert" advice, just my personal experience.
Let me start off by saying that I did purchase my road bike from a bike shop and I did have them fit me to the bike.
At first, I did not having of the arm/toe issues that you are having. I had been riding my mtn bike for about a year on the road, and the transition was very smooth. I went from struggling to finish 15-17 miles on the mtn bike to breezing through 20 miles the first I rode the road bike.
I first started to notice the arm/toe issues that you are talking about once I started increasing my ride time/distance. I went from 20mi to 30mi and I would have arm fatigue/numbness in my ring/pinky fingers. Also, my 2 smaller toes would become numb, as well.
For me, it was more of a conditioning problem than it was a bike fit problem. Eventually, I could do a 50mi ride and have no numbness, etc. 2 wks ago, I rode for the first time in about 6mos, and, once again, at about mile 11, my toes were numb and so were my fingers.
I know I kinda rambled on, but I hope it made some sense to you.