There is a major difference between GAPS and SCD. SCD is already proven while GAPS is still in the experimental stage.
SCD has been an established medical procedure since the early part of the 20th century. Data was collected by Dr S.V. Haas and other researchers of that era. Data showing the efficacy of SCD was published in academic journals in both Europe and the US.  Later, in her book Elaine Gottschall presented more evidence for SCD.
The diet advocated on the GAPShelp Yahoo list is too new to be more than an experiment. (the GAPShelp Yahoo list is the official list for the GAPS program). Despite a statement that GAPS simply springboards from earlier excellence to offer results even more spectacular, no data exists as proof that it is better than SCD or even as effective as SCD, nor is there scientific proof of all the changes with which GAPS contradicts the advice of Dr.Haas and Elaine Gottschall.
SCD and GAPS do share common elements which is not surprising since the latter is promoted as based upon SCD:
1 Certain carbohydrates feed microorganisms (Dr. Campbell-McBride was influenced here by Elaine Gottschall)
2 Both diets display an interest in fermented foods, broths, grass fed meat, organic food and juicing. [These beliefs were influenced by WAPF diet ]. Such elements debuted on SCD in 2000, when a group of SCD enthusiasts led by biochemist Seth Barrows proposed "enhancements" to SCD.
Seth founded "Healing Crow," a Yahoo Health list. Elaine Gottschall, became an active participant. The Healing Crow list is no longer active but many of its recommendations are posted to the Pecanbread list and its website. There is a link on the Pecanbread website called Enhanced SCD. The suggestions are optional for SCD. There is a small group of patients who do not always improve with standard SCD and heal better with organic foods.
It is vital to be aware of the major differences between Enhanced SCD, Healing Crow ideas and GAPS. Enhanced SCD and Seth's Barrows Healing Crow protocols adhere to the principles established by Elaine Gottschall; GAPS' do not.
There are numerous differences between SCD and GAPS.
New elements that have recently been introduced to GAPS are incompatible with Elaine's clear requirements. Changes that contradict the principles of SCD have been added by GAPS' moderators and members of the GAPS Yahoo list. We will refer to the diet that was developed on that list as the GAPS Yahoo Diet.
Dr. Campbell-McBride does not participate on the GAPS Yahoo list. Changes were made by people associated with the list.
We do not know how Dr. Campbell-McBride collects her data. Her practice is not accessible on the internet but the GAPShelp list is. Although little data has been made available by GAPS Yahoo, it matters since more parents appear to visit the GAPS Yahoo list than visit Dr. Campbell-McBride's office.
Before SCD was introduced to Defeat Autism Now (DAN)
carefully checked the science behind SCD. It is hoped that DAN will evaluate the science behind GAPS in order to understand where it is differs from Elaine's findings and instructions.
We believe there are major advantages in following science based Pecanbread Protocol rather than GAPS. There is only limited time and space to highlight a few of their changes. It would require years to research scientific details involving all the differences.
The moderator of the GAPShelp list states that one of the main differences between Gaps and SCD is the fact that GAPS does not require the strict adherence demanded by SCD. 
Strict dietary compliance is a success requirement for many children with autism who follow either GFCF or SCD. Infringements are equivalent to allowing a little bit of peanut to a child with severe peanut allergy. The scientific evidence for strict compliance while following SCD is OVERWHELMING.
Click here to view an example of this.
Click here to view evidence
Click here to view additional evidence
GAPS allows peanut butter at stage 3.  Standard SCD allows peanuts.
Following Elaine's passing, it became apparent that peanuts are a main cause of problems on SCD. Now, Pecanbread prohibits peanuts particularly for children.
Most peanuts contain aflatoxin, a toxic mold. A research paper states that the COMBINATION of the bacterial toxin, LPS, together with aflatoxin creates liver damage. People with IBD or autism tend to have very high levels of LPS, before they start SCD. The LPS levels may not go down quickly. There are elements in a large category of foods known as goitrogens that block iodine. Two goitrogens prevalent in the American diet are contained in peanuts and peanut butter.
Research article and more discussion about peanuts.
We have had several people report to us that they could not tolerate the GAPS diet due to its high fat content. We do believe that good fats are very important for brain development and for the immune system. We commend N for recommending them. However, many people with severe bacterial infections, have fat malabsorption and cannot tolerate the good fats during the early phase of the diet. This is due to the fact that bacterial toxins impair fat absorption.
Proof that bacterial toxins impair fat absorption
More scientific discussion about the differences between the Pecanbread Protocol and GAPS
Extensive research has enabled us to detail the scientific reasons why SCD is more effective than GAPS.
Click here to view it
Haas, S. V.: Value of banana in treatment of celiac disease, Am. J. Dis. Child. 28:421, 1924.
Treatment of Heubner-Herter's disease with bananas, sour milk and junket, Arch. f. Kinederh. 84:144, 1928.
Kleinschmidt, H.: Chronic Diarrhea in children, Jahresk. f. Aerztl. Fortbild. 13:16, 1922.
Gottschall, E (1994). Breaking the Vicious Cycle: Intestinal Health Through Diet (Revised edition ed.). Kirkton Press. ISBN 0-9692768-1-8.
"Philosophy: Breaking the Vicious Cycle promotes ‘fanatical adherence’. GAPS is more accurately described as a list of recommendations, from which each patient will develop a personalized program."
"Add pancakes, starting from one pancake a day and gradually increasing the amount.
Make these pancakes with three ingredients: 1) organic nut butter (almond, walnut, peanut, etc);"