With fiberglass, you don't have to worry about the weave because you will sand and paint over the working area to complete the project.
With carbon fiber, your entire piece is exposed and cannot be sanded or painted over to hide any flaws in the layers. So once you lay it down and then form it by stretching or pushing into the form you want it at, your are pretty-much set with that.
In addition, by stretching your Carbon Fiber material, you are distorting the weave - it becomes much more obvious when you are dealing with large pieces such as engine side cover or hoods.
Another thing to think about - is the material you use to seal your pieces. If you have ever looked at Carbon Fiber hoods that have been installed for daily driving, over periods of time, the Hood
will turn 'smokey' white or 'creamy' yellow in different places. If there are air bubbles or pin-holes in your product because they havent been set correctly, these areas will be the first to change color. Unlike fiberglass, you cannot just fill the pinholes on clear coated items with putty.
The correct coating must also be chosen correctly - if you use low cost material, your parts may begin to crack during or within a few weeks of completion. If you use an inexpensive gel coating that cannot hold up to high heat (such as your engine), your pieces may warp and become deformed.
I would suggest that before you tackle this, purchase some less expensive material and practice on that piece first - you will soon know the difficulties involved and why some retailers sell certain pieces for much more than other pieces (the price is in the manufacture difficulty level)
But by all means - please do try making your own pieces - you could be much better at working with material than someone who has less perfection skills
you are doing the right thing - ask allot of questions, test out your options and read what many others have noted in their articles... people dont become "masters" over-night - they practice and over time, they get better and better than everyone else who does not practice.
Theres a book in bookstores, "Fiberglass and Composite Materials" by Forbes Aird (thick magazine size) thats good.
This page might give you a head start (its not automotive related - but is a crash course in working with fiberglass)http://www.thinkcomputers.org/beta/home.php?x=guides&id=6-1