YA trilogy. Read it around 2004-05. Random find at the library, don't know the publishing year.
The first book has 2 clones (male, age between 10-16) living in a very controlled environment but separate from each other. They eventually find out about each other and escape. Vaguely remember that the first book had a title like Race Against Time.
Second book title had something to do with the number 2; the title had something like the word "double" in it.
At some point in the series a third clone is found. There is also some sort of virtual reality and some characters in the VR who keep helping the clones. Vaguely remember this part in book 2 where one of the clones is going through a "tunnel of love" type place (not sure VR or reality) and at the end of it he meets a girl who helped him in the first book. Possible he has a crush on her too.
Also remember a line from the second book where someone says that the "clones standout too much because their faces are identical".