Correct, Modafinil is not an amphetamine. It is distinct from other psychoactive substances, and we don't fully understand its mechanisms of action, how it affects the brain, or why it works. It's normally classed a 'eurogic' or 'wakefulness-promoting agent', and it (+derivatives) is the only drug of that class.

Long term effects are tolerance, and.. not much else. It has to be cycled regularly. If you abuse it or fail to socialize/have fun enough it'll end up making you feel like a zombie. It's been in regular use for a decade and a half, I haven't heard of any serious issues.

The main risks are the first time you take it. If you're allergic you can have some very serious reactions. In addition, if you're in a high-risk group (low immune system, etc.), you want to avoid the slight risk of SJS/TEN is can cause. SJS/TEN is probably the most terrifying risk, although it's extremely rare, and hundreds of other drugs can cause it too.

Each of these substances are amazing, but not without some danger.

I have a friend who has taken it every day for the last 2 years. No negative side effects except when he doesn't take it, he feels like he is not performing at his best.

The major concern with Modafinil is that we just don't know what the long term side effects are. That's the risk you take.