Thank you all very much for your replies, it put my mind at ease for sure!

All the check points I've gone through in the US were really impeccable and I'd dare say I was a very lucky one based on some stories I've read on these forums (young female flying alone). They were a lot more anal at Lisbon and I even commented to the TSA guy at Newark that I had to remove every single thing from my bag and break it apart as far down as possible and the guy said "Yeah, we're a lot more laid back here, we're not here to harass people".

What would that secondary inspection consist of? I don't mind taking the 3 small lids on my laptop, exposing the CPU, memory, HDD and a good chunk of the motherboard but more than that and I'm afraid they'll either damage my computer or make me lose my flight.

Thanks again for your answers.