Removing InnoDB indexes causes database table almost not accessible and slow
5.1 ALTERs work faster if you perform them simultaneously:

ALTER TABLE mainData
    DROP INDEX foo,
    ADD INDEX (col1, col2);


You can perform that in the UI window that lets you perform arbitrary SQL.  It will be twice as fast (in older versions) than doing the DROP and ADD separately.  This is because each ALTER (not each clause in it) involves a complete copy of the data, plus a complete rebuild of the resulting set of indexes.