if your torsion shaft is moving back and forth, it shouldn't be. The drums limit the travel if they are properly tightened and the bearing plates are tight. Here's the sequence of how it should be set up from scratch:
Start with unwinding the tension on the spring. If you don't know how to do this, then don't. Get someone who does. It's the one thing on a door that will get you hurt. Once the spring is unwound, start with either drum, it doesn't matter which one. Let's use the left for example. Make sure the drum is all the way against the bearing plate with no play in between. Make sure the cable is attached and then wind the drum so it takes up the extra slack. Take a pair of vise grips and put it on the torsion shaft with the non-adjustable handle of the grip hitting against the wall or ceiling if its close enough. Just use enough pressure to hold it on the tube without deforming the tube. What you are doing here is maintaining the tension on the cable of the left drum so it can't unwind. While you're at it, take another vise grip and clamp one of the rollers to the track with moderate pressure. You are just trying to prevent the door from moving. Now go over to the right drum and loosen both pinch bolts. Move the drum over against the bearing plate so there is no slop. You can give the shaft a push to the left just to make sure there is no slop. Now make sure the cable is still attached and turn the drum to take up the slack. At this point, since you have the shaft clamped from turning, both cables should be pretty much equally taught. Tighten both pinch bolts snugly. Leaving the vice grips on, wind the spring. If its a 7' tall door, 7 full turns should do it. Once the spring is wound but before you tighten the two pinch bolts on the spring, take the winding bar that is not still stuck in the spring, and tap the bottom of the spring from one end to the other to help it lengthen itself so it lays straight and not up and down like a snake. Now tighten both pinch bolts carefully, while still holding the spring with your inserted winding bar. Once both bolts are tight, using both pinch bars, carefully release your bars control of the spring. It should move just a smidge and put tension on the shaft, which in turn will move your vice grip thats on the shaft about 1" away from the wall where it was sitting against. release the top vice grip, then the vice grip on the rail. Keep a hand on the door when you release the second vice grip. It shouldn't move. Now run it up and down by hand, keeping control of the door. It should move smoothly, without clunking. The shaft should not move back and forth, just rotate. If you lift the door about 4' off the ground you should find the balance point, where the door should just sit there and neither want to go up or down. Move it all the way up by hand. When you let go, it should hold itself up in the opening without falling back down. If you let go when the door is at the balance point and it wants to fall all the way back to the ground, then the spring may need another 1/2 turn to add some more tension. If you need to to this, make sure you put the two vise grips back on like before. If you don't, with only one spring on the shaft, the shaft will unwind when you loosen the pinch bolts on the spring and make a mess of the cables and scare the heck out of you. If you have the door at the balance point and when you let your hands off it, it wants to shoot up into the open position, then there is too much tension on the spring. You would have to take a 1/4- to a 1/2 turn off. This is all assuming you have the correct strength spring on the door. Let us know what happens.