When did Islam spread to the Phillippines?
Are the Muslims in the Phillippines culturally closer to the rest of the Phillippines, or neighbornig Muslims in the region?
How were Muslim Filipinos affected by Spanish colonization? Did Muslim Filipinos support Emilio Aguinaldo? How were they affected by American control? Were they affected by the Japanese occupation?
When the Phillipines became more independent, did Muslim Filipinos want to be part of the same country? Wikipedia says they have an autonomous region. What level of self-rule do they have?
Not exactly my area but I can at least answer a couple points.
When did Islam spread to the Phillippines?
The arrival of Islam to the Philippines (one "L") is attributed to Islamic merchants in the late 14th century. There was a healthy trade network between the Far East and the Middle East at this time. Heavy proselytising lead to a high number of conversions over the following decades. Islam spread early and quickly and, prior to Spanish arrival in the 1500s, the Islamic sultanates were fairly powerful.
How were Muslim Filipinos affected by Spanish colonization?
The Spanish themselves were big on conversions (leading to the majority of Filipinos being Roman Catholic today). There was always tension and fighting was not uncommon during the Spanish colonial period. The biggest impact of Spanish colonisation on the Muslim population is the significant decrease in practicing Muslims.
That's all I know the answers to. Hopefully someone else can come and address the other parts.