I have been dealing with candida for longer than I can remember (having a MRSA infection treated with IVBP Vancomycin in 2005 only served to expontentially compound the issue!). I also have severe heavy metal toxicities and debilitating GI issues and food intolerances (as well as FMS/CFS, IBS/IDB, GERD, severe gastroparesis and early satiety, low wt, osteoporosis, hormonal/neurotransmitter imbalances, hypoglycemia/insulin resistance, hypothyroid/adrenal fatigue....)

The antibiotics will account for several of your problems such as the IBS/IBD, Candida overgrowth, GERD, malabsorption and gastroparesis.  The best way of dealing with this though is with live cultured foods such as kefir, miso, tempeh, sauerkraut, etc. to reestablish the flora and prebiotics to feed these and the surviving beneficial flora in your intestines.  I don't care much for probiotic powders and capsules since there is no way to determine their viability.  For instance, simply shipping them in the heat can damage probiotics.

Fibromylagia has been linked to low ATP levels and low serotonin levels.   Magnesium malate elevates ATP, while the flora of live cultured foods provide B₆ that aid in serotonin production.

Osteoporosis is best treated with silica and vitamin C sources as osteoporosis is not from a mineral loss, but rather a collagen loss.

There are different forms of hypoglycemia:

http://curezone.org/forums/fm.asp?i=1459218#i

With adrenal issues and with insulin resistance you likely have both forms of hypoglycemia.  Here is a post on supporting the adrenals:

http://curezone.com/forums/fm.asp?i=1527351#i

For the acute hypoglycemia I recommend chromium polynicotinate (not picolinate) 200mcg 3 times daily with meals.  This can also help with the insulin resistance along with magnesium malate.

My Chiro is going to have me start MMS. I'm kind of nervous to start it, for I've read that it is quite strong and produces some severe side effects. I'm also underweight (thanks to the GI issues and food intolerances), so I cannot afford to lose weight. However, all the issues I'm dealing with make it impossible to gain weight due to the malabsorption it causes, as well as the gastroparesis, constipation, GERD, no appetite/early satiety and repulsion to food.

I've tried nearly EVERYTHING to get the candida (and possible lyme) under control, but nothing works.

The only way to get Candida back under control is to reestablish the flora.  Simply trying to kill Candida will not work. 

First of all Candida albicans is a normal part of the body.  But this microbe is dimorphic meaning it can exist in two forms.  In an acidic environment the Candida remains in a benign yeast form and its growth is inhibited.  The acidity that keeps the Candida in a yeast form and controls its growth is provided by beneficial flora inhabiting the body.  When the flora levels decline, such as with the use of antibiotics, the pH of the terrain becomes more alkaline increasing the growth of the Candida and converting the Candida in in to its pathogenic and aggressive fungal form.

Here lies the problem with trying to kill Candida.  You can never kill off all the Candida in the body.  And trying to kill the Candida does not change the pH of the terrain.  Therefore, any surviving Candida microbes will simply grow back in a dangerous fungal form at an accelerated rate due to the still alkaline pH.

Getting Candida back under control requires restoring the pH, which is done by restoring the flora.  And the best way to do this is with cultured foods and prebiotics.

Thus, my chiro wants to try this route (I also read it can help with certain metal toxicities too, among many other issues!).

MMS can precipitate iron and some other metals.  But it can also induce hemolysis among other side effects.

Any thoughts about how I can maximize my treatment while taking MMS?

I recommend avoiding MMS altogether.  I addressed this in a recent post:

http://curezone.com/forums/fm.asp?i=1859584#i

Any supplements I should take with this and any that I should avoid?

I would avoid the MMS.  You cannot take supplements at the same time as MMS as the MMS can oxidize the supplements and there are possible adverse reactions between the organic material of the supplements and ammonia in the body and the chlorine released by the breakdown of the unstable MMS, which can lead to the production of toxins and carcinogens.

I have read about people taking MMS in capsules... how do they do this?

I have no idea.  Chlorine dioxide is a gas, not a solid.  They must be using some other chlorine compound.

What should I do about my diet? My Chiro recommends a 40% protein/30% carb/30% fat diet.

There is more to it that just percentages.  There is the issue of types of protein, carbohydrates and fats.  For example, white sugar is a carbohydrate, but I would not recommend 30% of your diet being white sugar.  Same goes for I would not recommend 30% of your diet being margarine, which is a fat.  There are good and bad proteins, carbohydrates and fats.

For protein I recommend primarily plant proteins.  Chlorella is a great source being about 3 times higher in protein than beef.  Chlorella also helps to build up the flora and remove heavy metals as well as provides a good source of magnesium.  Nettle leaf is also a good source of protein and helps to support the adrenals and thyroid.

One of the biggest problems with animal proteins is that they are pro-inflammatory due to the inflammation promoting arachidonic acid.  Animal meats are also more prone to be contaminated.  Especially with hormones, antibiotics and heavy metals.

Any suggestions as to what to eat in terms of meal and snacks (I have a limited diet and cannot have dairy, red meat, wheat/gluten, peas, most grains except for rice, fruits, and sugars.

Why would you be eating a diet with fruits and sugars with Candida overgrowth?  And grains contain phytic acid that binds heavy metals removing them from the body.

As for things to eat, for animal protein fish is the best.  I recommend tilapia, cod or haddock as these are the least contaminated.  If you want poultry look for organic.   Other foods I recommend are yams, jicama, yucca root, nopales, seaweeds and beans are all good choices.

How long do I do MMS? What is the general protocol?

Again, I do not recommend it at all.  Also keep in mind that you mentioned having hypothyroidism.  MMS will further suppress the thyroid as the chlorine is an antagonist to iodine.

What supplements do I do AFTER the MMS?

Again, avoid MMS.

Should I continue the MMS at a "maintenance dose" and if so, for how long?

Again, avoid MMS.

Any thoughts on Probiotics during this treatment?

Yes, use them in place of the MMS.  They are safer and you really need to reestablish your flora.  But again use live cultured foods.  And don't forget that you need to feed the flora with prebiotics.

I am currently taking:
-multivitamin
-vit D (2000-4000IU)
-Magnesium Malate (for FMS)600mg Mag Malate + 3000mg Malic Acid
-Thorne Cortrex (adrenals)TID

Thorne Cortcex is a glandular supplement.  The long term use or high dose use of glandulars atrophies the glands they are substituting for, which is why I recommend avoiding glandulars.

-Biotics GTA Forte II (thyroid) TID

Also a glandular and so not recommended.

-Biotics Iodine drops (150mg)
-Biotics Meda-Stim (thyroid)
-Standard Process Tuna Oil (4 caps)

Tuna are predatory fish and thus tend to have very high levels of heavy metals.  Some heavy metals, such as mercury, have a very high affinity for fats like the oil in fish.

-Probiotics
-Aloe juice (3oz)
-Vit C 2000mg
-Lifetime liquid Mag/Cal/D (to help with BMs)

Calcium contributes to constipation.  Magnesium promotes bowel movements.

-and for meals/snacks: 1 Renew Life Digest Ultra,

These are digestive enzymes, which pose several problems.  First of all the use of supplemental enzymes shuts down the body's own ability to generate its own enzymes.

Another issue is that the Digest Ultra also contains pectinase, cellulase and hemicellulase that create more sugars that can feed the Candida while starving the flora needed to control the Candida:

http://curezone.com/forums/fm.asp?i=1555407#i

2-3 Biotics Betaine Plus HP (HCl)

Both the digestive enzymes and the betaine HCl will destroy your probiotics if taken together.

I really need help.... Ive tried everything and am praying this helps, for my quality of life is beyond sucky. :-(

A lot of the problem is that you are addressing so many of your issues in the wrong way.  Not everything is compatible, and atrophying the glands, destroying the probiotics as well as digesting the fibers you need to feed your flora are all counterproductive.  So is taking tuna oil when you already have high heavy metals.  Same goes for taking MMS, which will suppress the thyroid when you are already hypothyroid.

Maybe you need to back off of most of what you are taking and focus on one thing at a time, such as restoring your flora.  Restoring the flora will help address many of your health issues.