jairaj - glad you're enjoying it! now to answer your questions;
I have researched various homemade bikes to see how many layers that each of them used, also sheldon browns site has a carbon bike project on there which was useful to look at, as for computer simulations (FEA) I didn't do any and I don't have a huge amount of experience, so I'm just using my best judgement on where I think needs extra strength and where can do without.
For the suspension design I bought Linkage X3 software (about £15 if I remember rightly), it was well worth it as I have been able to calculate travel, leverage ratios and the overall side profile look of the bike. I have roughly copied a 2009 scott sparks geometry but have used elements of the rocky mount element from around that period too, I have also made a few modifications to suit the parts I have. I also used NX8.5 to do the final details in the design.
there is a little bit more info in the designing in part 1 + 2