Dear Lonny,
Your description implies that your son was functioning OK and then developed the eating and toileting problems. If this is the case, it's probably fair to conclude that the behaviors are symptomatic of the turmoil brought on by the changes in his life.
Relative to the mealtime difficulty, simply present the food and stay away from struggles about what he'll eat and what he won't eat. If he doesn't wish to eat the food, let it go. You needn't prepare alternative items for him. Some people are comfortable with permitting a standard 'option' (e.g., peanut butter and jelly sandwich), but by no means is this required. Engaging in struggles with his stepmother will only exacerbate the problem.
Relative to the encopresis and toileting behaviors, it's important to know if these have been chronic problems or represent regressive behaviors (indicative of emotional upset). Proably the circumstances that resulted in your children's moving from their mother's home to your home are instrumental in the development of your son's behavioral problems. You would be wise to seek some professional assistance and not permit too much more time to go by. He needs some support, both within the home and professionally, to help him with these major changes in his life. Remember, his world has been turned upside down.
I don't think you should be so hard on him. The fact is, children will eat when hungry. If he doesn't want to eat it don't worry. If it is a power play with the stepmother, she will loose if she stoops to his level; I have been in your shoes and I have been in hers'. Offer him the same food as the rest of the family and let it rest there. He will eventually eat. Right now it sounds as if it may be a competition.
As for messing his pants, is this staining or messing? Staining often stems from an active busy little boy with much going on. Patiently work with him and it will get better.
The child may be having a problem with his stepmother being his "authority" figure. He has two parents and you need to work on this together. Remember:divorce and remarriage is very hard for many adults. Imagine how difficult it can be for small children. In any case, I am a parent and a step-parent. The road was a rough haul but well worth the rewards after 15 years.