As to the neck woods, you could just take the clear board, and build a neck with a scarf joined headstock and stacked heel. You'll find use for the clear portions of the knotted piece.
As to your top, you'll be fine. It's not like strings are pulling across the grain. Also, the configuration of the X brace, tone bars, finger braces, transverse brace is such that they support the soundboard cross-grain and do not leave any long lengths of unsupported long grain. I've seen tops of finished guitars with even more cracks, repaired and doing well.
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On a side note, My thoughts on woods for beginners are in opposition to some. Maybe I can see practicing some new technique on a piece of scrap or cheap wood, but not on the actual guitar. Unless you split and resaw the wood yourself, cheap wood usually will have problems that you'll will have to deal with at some point and time. I also think that for the most part, the cheaper the wood, the less worried you are about ruining it, therefore the less careful you are with your work. A big argument I hear in favor of it is that "the guitar sounds fine" or "the guitar sounds like a guitar." Which is fine if one's attitude is the same as building, say, a scale model car. Maybe the lure of building a guitar is part the curiosity of the processes involved, but I'd hope that one seeks a guitar that maybe sounds better than "fine" or even a cheap guitar - otherwise just buy a cheap guitar! The other argument is that "Taylor and Benedetto made pallet guitars that sound great!" Well, they can do that because of their experience. Making a guitar out of pallet wood won't guarantee your guitar will sound like Benedetto's just as much as using the finest tonewoods.
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