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You are right,
there are many different programs that will do this for you. Alot of people like to use MaximDL, others include Nebulosity, CCDsoft etc etc.
As for guiding and PE
Guiding will hold onto a star untill either clouds come, something bad happens or you have to flip over to the other side of the meridian, but you wont have to do that so much as the forks allow you to track from one side to the other.
PE is Periodic Error, its basically defects in manufacturing that is inherent in all mounts to some degree. If you are to look at most GEM they will state that the PE is +- 5 arc seconds or something like that. What they are actually saying is that if you have perfect polar alignment and let the mount go un guided the star will drift a maximum of 5 seconds of arc either way. So as you can well imagine thats why people try to get that number as small as possible so that the guiding is just nudging the mount here and there not going all out just to hold onto the star and then when the wind pops its head into the mix the guiding cant hold on and then you get eggy stars. It will not accumulate.
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