[Simbal]

for your problem, try to load a older save when you are asked to Instant Jump to Destination or something like that, click no and free roam till you got enough credits to buy Good Equipment, or even search hidden stashes (A thread on hidden stashes is here somewhere)

for your question, I don't really know about the bonuses and the difference exactly but i think it does little difference (even if not noticeable)

for the repairing modules, here are the actual heal rates for all Repair modules

- Flight Repair Units
Cleric = 1HP/s
Reedemer = 2HP/s
Sigil = 4HP/s
Phoenix = 10HP/s

- Repair Units
Gnome = 1HP/s
Cobold = 2HP/s
Gremlin = 4HP/s
Nannite = 8HP/s

- Emergency vessel repair Systems
Troll = 10HP/s
Werewolf = 20HP/s
Lycanthrope = 50HP/s
Ogre = 100HP/s

- Base Modules
Chrome = 1HP/s
Nickel = 2HP/s
Vanadium = 5HP/s
Tungsten = 20HP/s