The ship problem has been discussed and addressed in this thread:
http://www.twcenter.net/forums/showthread.php?t=197982
Rebuilding ports costs just the same as building them - if you've captured the city and destroyed its port. I do not know what is the situation if you use an assassin to sabotage the port(if at all possible). I would imagine that the building is just damaged and could be repaired in 1 turn for less money than it costs - as it is with siege damages.
Quinn is working on buffing Parthia for ExRm 4.0, there is also a special thread about the Ptolemies. The Carthaginians should not make naval invasions on Capua anymore, not with the latest hotfix.
If you try the changes in ship stats, bear in mind that I geared them mostly toward medium campaign difficulty - you might want to increase recruitment/maintenance a bit more for hard. And please post what your experiences were - I'm sure Quinn could use the feedback for 4.0.