When I transitioned to the bent a year ago I continued wearing my Shimano MTB shoes with my MTB pedals.  My distance has increased over the past couple months and I recently completed a 204k with the LSR folks.  As my distance has increased so has the pain in my feet, thus I'm looking for some wisdom from others who have gone before me.  My shoes and pedals are in very good shape, cleats are all the way back so I have no issues here.  I do know that as long as my distance don't typically get above 40 miles my feet don't bother me.  After finishing the 204k I could not walk without pain in my feet and they hurt for two days(some would say no wonder), both rides(45, 31) since have resulted with pain in my feet.  Before the increase in distance training I had no issues at all.
 
Today I did some research and discovered an article that addressed the use of MTB shoes and pain, the recommendation was go to a road shoe that is very stiff and perhaps moldable insoles.  I know there is a tremendous amount of wisdom in this forum and many of you have done the type of distances I am doing so I solicit your input and recommendations in all areas.  We know that recumbent riders are different from what we commonly read so you are the experts.  For what its worth I am currently riding a P-38 with Time Pedals and Shimano M087 shoes and typically ride a cadence of 82-86 at speeds of 16.5-18 for distances of 30-75 miles, I tend to slow a little at 100+ to 16ish but kee the cadence between 82-84 .
 
Thanks in advance for the assistance.

Yep, keeping your feet from hurting can be tough. I always had hot foot troubles from a long ride, and it got worse after nerve damage from chemo.  
 
If you plan on staying with MTB shoes, I recommend Bebop pedals. Their cleats spread out the pressure better than any other MTB pedal. Road pedals and shoes do a better job, too, but they aren't very friendly for walking, or even keeping your feet from slipping when you put them down at a stop.
 
Get good comfortable shoes, too. My Sidi Megas (the Mega is the wide version of a Sidi shoe) are extremely comfortable.
 
The other thing I recommend is lacing (or strapping, as the case may be) your shoes very loosely. I always liked mine good and snug, but I found out that I get a lot less foot pain on long rides with them loose. If it causes my socks to wear prematurely, then so be it, I say. Keeping foot pain away is more important.

Quote from Phantom Rider on Jul 8^th, 2013, 8:55pm:

To illustrate the statement that "everyone's feet are different", in my case, the stiffer the sole, the worse my foot problems are. I have worked on my foot issues for years and have had a reasonable degree of success but still when I do an ultra race that requires a high level of constant power output (such as constant 25-30mph headwinds), I have problems and just have to cut back on the power when my feet light up in pain. By 'light up' I mean that it feels like someone runs across my feet with a propane torch.
 
In short, I have to modify my shoes (usually not difficult) to move the cleats much further back and then strategically modify the inserts, starting with a hand-wrapped bottom (cheap) insert with a high-quality insert on top of that. I wrap the lower insert with short strips of elastic bandage. This allows me to fairly easily shape the insert and try it out over time, moving things around until I'm satisfied. Using a stiff sole makes it harder to shape things to fit as it tends to concentrate pressure in a few immovable areas.
 
How well does this work? Well, just last week I pulled the pedal insert loose on the crankside of my Lightning carbon cranks. I was pulling about 950 watts in a slight uphill sprint in traffic at 34mph when I noticed my shoe starting to turn out. When I got to a place where I could stop I saw the cranks had started to delaminate around the insert.  I've put over 50,000 miles on these cranks in 3 1/2 years, abusing them in this sort of way almost every day during that time so I figure that's a pretty good product. Plus Lightning is replacing the crankarms for $200 so good customer service in my mind.