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The solar system is not to scale. Neither is anything else it seems. Each warp has been getting longer as they test to see how far it can go. Each warp is generating basically a limited time wormhole to a preselected area of space-time. They have to be accurate with the calculation and timing of the warp (at least in Yamato's case) or else they might break the engine, are miswarp someplace they don't expect, or get caught between dimentions (Episode 10).
There main limitation is knowledge. This is Earth's first Wave Motion Engine equipped ship. They don't know all the ins and outs of how it works yet. The Gamilas do as they seem to be able to warp much faster than Yamato can, and they can track a vessel that warps.
Another problem is that the warps strain the ship and crew. The longer the warp the more stress on both. As some point they are likely to break something if they push the warps too far.
As for how often they warp. Probably the ship needs to build up power again to warp (that seems to be the older explaination). They use to warp once or twice a day if I recall. When they warped into the rift they were losing power. The thought of warping out was never brought up (probably they couldn't) and using the wave motion gun drained the ship of about everything it had left when usually they build up energy to restart the systems after the guns fires so that it does't leave the ship helpless.
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