What type of modchip do you recommend?
ANSWER: An internal modchip as it reaches more controllable parts. The most popular modchip is NEO2.2. Everythingis booted via a swap method and no one who has installed it properly and used CloneCD to make copies has had a problem recorded on the forum so far as I know. I use an OrigaChip because I want to boot import originals.

What are the processes of getting it installed (or is it something that i can install myself?)
ANSWER: You need to be a good solderer to do it yourself. You'll need a 1mm tip etc. Best to get it done by a solder whizzo.

Are protected games impossible to copy and play?
ANSWER: At this time, CloneCD makes 1:1 copies and brings the protection over to the copy. Your reader/burner must be RAW-DAO+96 compatible to properly treat sub-channel data.

do you know any specific games that are protected?
ANSWER: Too many to list. www.ps2ownz.com has a database of games and patches.

my main target right now is grand theft auto 3.
ANSWER: Until you've got your head round the basics, you'll find DVD ripping to be a minefield. DVD copying will need a DVD burner and the result will work with the NEO2.2. If this game is a must for you, buy it!