Using aftermarket parts can significantly improve the model kit. It just depends how far you want to go. As this is your first armour build and not knowing how much model building you have done I don't want to sound condesending but would like to offer what I think is some sound advice.
Welcome to the dark side of modelling. Armour building can be both easy and hard to do. like all modelling there is lots of research to do on top of that already done by the kit producers, especially if you are looking to build a perticular vehicle.
Don't overload yourself with your first armour build wih lots of aftermarket parts and add-ons. Doing this can lead to frustration and in the end disappointment.
THe reason why I am saying this is that although I don't know your level of skill, but you have said that this is your first amour build then my immediate recommendation is the KISS system (Keep It Simple, Stupid). You have to build up your skills slowly and don't try to run before you can walk especially with armour. Working with an armour kit is pretty easy but working with etched brass sets isn't. you have to develop the skills for bending metal and the use of cyrowhateverthenameis (superglue). One wrong move and not only is the part glued to the wrong place permanently but IMHE me too!
you have a lifetime to develop these skills and produce stunning builds. Keep this armour build simple and out of the box and then, as you already have a Jagdpanther etched set get that kit and have a bash at using the set. Don't worry about tracks at the moment because you can always add them at a much later date.
looking forwards to seeing your build progress on here.
James