I'm probably too late here. But for PvE the only upgrades I recommend are copper, storm chaser, and cargo 3. Btw, I agree about the look of the chains on coppers.
If the reason you're looking at skull and bones is for damage, storm chaser does much more of it, while also being faster and more maneuverable. The biggest complaint I hear about it is the way it looks, if that's the case for you, your only option then is skull and bones. None of the other upgrades are even worth considering in terms of damage.
I don't think fortune hunter is worth it on any level, but if your heart is set on it, I fully agree with Stout- get IV and stop there. You get the same speed, turning, and cargo as fortune hunter 6, and still 20% more armor than stock. If you go all the way to fortune hunter 6, it'll cost 285,000 gold, 2,400 iron, and 450 steel... and all you gain is 17% more armor and 10% stronger broadsides.
All that being said, if your heart is set on something, then by all means get it. It's your ship after all!