truthseeker,
I got one of these too for xmas and have learned soooo much about helis in the last month.
Yeah the stock flybar is metal and bendable, it should be as straight as you can get it but there are a couple things that can cause wobble:
1. Did you lose the camber link? There should be one link from the flybar to the upper blade, this is not optional, and is the most likely candidate, see pics below.
2. The flybar MUST be on the leading edge of the blade. That is, as the blades spin, it must be in front, not on the trailing edge. (It's only possible to get this wrong if you got the two-piece upper rotor head and it's rotated 90 degrees.)
3. Take off the flybar and make sure the rubber and metal are all the way out on the ends. Don't pull too hard, you will rip the rubber. grab it by the center plastic with two fingers and roll it in your fingers; if it's bent, straighten it as best as possible. Perfect is nice, but it doens't have to be. Now put a razor blade vertically into a piece of balsa wood or styofoam or something, get it as perfectly vertical as you can. Now try to balance the flybar on it without the camber link attached. It's OK for it to be **a little** out of balance, but if it's not, see if you can move the plastic dealio in the center one way or the other. They're usually very solid on there, but if it's bumped and slipped a little try and recenter it.
4. You can do the same with the blades, remove them and snap them together, you may have to put the screws in if you have trouble getting them to hold together. Put two razor blades in the styrofoam about as far apart as the ball ends, and balance the blades on the two razor blades. Sand equal bits off the leading AND trailing edge of the heavy side. I start with 50 grit for a couple strokes, then 100 grit for a couple strokes, then re-check for balance. See pic below.
If you do all that and it's still wobbling - it's a bend inner or outer shaft or both. Remove the upper rotor, then remove the two screws from the collet bottom of the shaft (under the BCX) and slide it out. Roll the shaft across a piece of glass with the head hanging over the edge, if you see any noticable wobble you can TRY to straighten it. If it's the outer shaft that's going to be a bit tougher to remove but same deal. It's not likely it;s the outer unless you crashed it hard and you'd have broken bits off the lower rotor head.
And a tip on the top rotor head: this has to be the dumbest part of the whole design (or smartest, if they want you to buy many many parts.) I've had my CX simply roll over in grass and it breaks off. So below is the coolest mod you'll ever find for the CX.
Next time it breaks (or try this with your old one!) find a piece of tubing that fits perfectly on the shaft. In the pic below, I used an old bearing from a rear axle of an AE truck or GT; the inner race fits PERFECTLY over the broken shaft. Now get some 5 minute epoxy and glue the collar on the shaft and the broken piece after that, be careful to perfectly align the broken peice with the top of the shaft. Let it set, and you'll never break another upper rotor again! The one in the pic below has been through five hard crashes now and the rest of the CX fell apart aound it.
Got LOTS more mods you can do to the CX, like folding blades, lights, etc. etc . . . this thing is flippin AWESOME and I love it.
But the top red one on the tail feathers blinks. Tap it right into your main power leads. 
