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thank you for your feedback :) to answer your questions:
1. on page 31 of the ship breakers toolkit you see the mention of a J9 drive in the section "dilatation of time" since its something for generation ships and something experimental i feel it fits well as it mentions they will never be seen again and MOTHER should have the plans of one in her memory somewhere and clearly want to keep control of her clones by going far far away.

2. well space is incredibly vast yes haha and with cryopods and the incredible large distances in space 3000 years doesn't sound that much to be honest. MOTHER  primary goal given to her was to first find a suitable planet, start the cloning process and colonize that planet. but with the failure of the jump-drive and only on basic propulsion she had no choice but to take the very slow route. MOTHER needed new material too be able to make a J9 drive so she took the risk to find a place where she could get credits, buy the material and build this thing before leaving as fast as possible.

3. yes you are right, its the same with some spots in APoF where its cyan on black, il do a alternative version to make it more readable and also printer friendly !