I really feel for your 6 yr old, and for you as the parents of a school-aged child who is having these issues. I'm sure your 6 yr old would prefer to be independent in all manners of pottying!
A few questions/suggestions:
1) Question - I'm curious about the diet changes... would you be willing to describe in detail what changes you made, what (if any) foods you avoided and for how long these changes lasted, how well you stuck to them? Is there any one food that your son simply loves, adores, and cannot live without?
2) Suggestion - this is perhaps a bit of an "out of the box" approach, but it could be quite effective on many levels (for your son, for you as the parents, and for your infant both in the short and long term/prevention of future bowel issues), but have you considered having your 6 yr old help your 3 month old learn to use the potty? This would be a really positive role in which to include your son and would also really highlight/reinforce in a very experiential way for him the universal signs that mean "poop is coming" (not only for the baby, but more importantly for him!) so that he may be more aware of and better able to attend to his own elimination (sensations, timing, frequency). Plus there's always the added fun and incentive of "everyone in our family uses the toilet" and the increased self-esteem that your son would likely experience in knowing he helped his baby sister learn to use the potty. (By the way, siblings are often very, very good at noticing when the baby has to pee/poop, they're quite tuned in and intuitive.) For more information on this out-of-the-box approach, please see:
viviente.com/2005/10/how_to_do_parttime_pottytraini_1.html
And there's a group of moms local to you who potty their babies, if you'd want to talk to someone or see a mom/baby pair in real life who practices EC:
groups.yahoo.com/group/CincinnatiDiaperFreeBaby/
I very much hope for your son that he will soon be able to independently control and be in charge of his own bowel movements - I'm sure that would be incredibly wonderful for him (and quite a relief and joy for you, too)! :)