My vote is get the best fitting, stiffest road specific shoe you can find. For the road (+widest most supportive road pedal). Put your mtb pedals back on that bike--use those shoes w/it. And the new road shoes w/the road bike.
I have some major foot issues and part of is attributed to too much ill pressure on the ball of my foot. I started just like you. Mtb shoes (all I had at the time) and my road bike w/mtb pedals. There is a campus pedal (one side mtb spd, and one side platform) on my mtb now. On actual mtb trails--it sux to no end. I want to be clipped in, but have to look down to see if I'm on the correct side. On tight switch backs etc., there is no time for that as you know (eyes ahead on the trail at all times to avoid crashing).
For road riding--you are not on and off like the mtb. Which I'm a weenie--so I'm pushin my bike sometimes and need to be able to walk/have grip on trails I can't clear all the obstacles.
If you are in a situation for road you will be walking, you can do a couple things. Look and SpeedPlay both make rubber covers for their cleats. If it's just a short in and out somewhere, you can pop em on out of a jersey pocket. Look came out with "new grip cleats". Which is suppose to help the walking safety thing. But, I don't really like it cuz I think the dumb rubber thingy makes it stick when clipping in and out--read: makes it harder.
Also, if you could find a way, a very compact light pair of flip flops would work for a longer stop. I saw on one bike website some type of folding shoe for this very reason (ad showed them sliding into a jersey pocket). Seems like I went to a salon once and they had some weird flip flips that did this after a pedicure to let the polish dry better vs putting back on a solid shoe over the toes. I saw a tourer guy whip out his flip flops out of the saddle bag and change to enter the shop. #1--he could walk fine then, #2 the shop was happy because the cleats were not tearing up their hard wood floors.
Shoe brands... Sidi's are great shoes if they fit you right. A nice stiff carbon sole, and a buckle system is good. Long story short, unfortunately my Sidi's contributed to my foot problem. My foot is shaped like a scuba diver's fin. Very square toe box area. Sidi's are more curved or pointy in the toes. This squishing of my toes is what contributed to my Morton's neuroma tumor (can be source of foot numbness). I have ordered/tried on many brands of shoes. The ones I *think* are going to be the winner for me are Mavics. I need the super narrow heel cup (which mens shoes w/typically wider toe room do not have, aka wider all over, including heel)--so ladies shoes fit good in that respect. The Mavics are more rectangular in the toe box--but narrow heel & overall lower volume foot (not too much vertical height to bump ankle bone). I have not rode in them yet (thus have holded off posting for full report), but I own the ladies Mavic Xena road shoe. Very light nice stiff carbon sole... nice secure buckle system... breathable roomy mesh for toe box area. Here is a link...
http://www.competitivecyclist.com/ro...04.2233.0.html
Good Luck!
EDIT: Here is a link that shows a couple styles of road cleat covers I mentioned. I have read some people complain they can fall off. But, they are pretty cheap--so maybe worth a try. FWIW. http://search.performancebike.com/se...w=cleat+covers
p.s. RE: the search function... it indeed can be overwhelming on here with a ton of helpful info... but I believe there is a way to do an "advanced" search... you could try my user name, *plus* your topic related to your pedal/shoe/foot pain issues and find all my epic blabbing about it. That might help narrow things down some for you. Plus, look at where the "key word" is listed on the forum... gear, health related, etc... that helps you narrow down which thread to pick first for viewing.