The best way I found to get materials for upgrading the Jackdaw is to replay Sequence 8 Part 1.
After doing this about 10-15 times I went from having around 200 metal to around 1900 and my rum and sugar went up a lot also. After selling all the rum and sugar I made about 50,000 which got me enough money for this trophy.
When you have enough of the materials you need, do NOT finish the mission or you will lose everything. Just restart from the checkpoint, make sure you have enough of what you need and then quit to the main menu so it can save.
All credit goes to It_doesnt_matter on Youtube, the video I watched helped me out and hopefully it'll help you too.