I had to solve a similar problem. I inherited a large source table from MS Access with nearly 15000 records that did not have a primary key, which I had to normalize and make CakePHP compatible. One convention of CakePHP is that every table has a the primary key, that it is first column and that it is called 'id'. The following simple statement did the trick for me under MySQL 5.5:
ALTER TABLE `database_name`.`table_name`
ADD COLUMN `id` INT NOT NULL AUTO_INCREMENT FIRST,
ADD PRIMARY KEY (`id`);
This added a new column 'id' of type integer in front of the existing data ("FIRST" keyword). The AUTO_INCREMENT keyword increments the ids starting with 1. Now every dataset has a unique numerical id. (Without the AUTO_INCREMENT statement all rows are populated with id = 0).