AHOY THERE, MATEY ! The advice you have been given is spot on(no pun intended) Any ship I build that has structure like yours gets ALL the locator pins cut off. Then , I carefully glue the bow together (as said, everyone starts there) and let it dry for at least a day or two,while making sure your glue application was very slight at best.I switched to the TAMIYA brand and haven,t regretted it yet.
Now that the bow is dry you need to move to the stern.Glue it together even if the pieces are out of whack.As long as they are the same height from top to bottom you have a home run.Let everything sit for another few days.Now , take some credit card thickness plastic, glue together the mid point locators. Make sure the hull at the flight deck is absolutely level,or that deck will NOT fit right.
When you have let everything set , then sand it all down by wet sanding with 320 grit.If you need filler ,use it now.After you get it all smooth then take a board.YUP,a board.About 24 inches long and wrap it in sandpaper and proceed to lightly WET sand the bottom ,so the ship bottom has a nice straight surface to bond to.
Don,t sand it to vigourously.Now glue on the bottom using TAMIYA masking tape spaced two inches apart then come back and tape in between the original tape.Now carefully apply TEENSY drops of glue.Let this sit for at least a full two days.When it comes to gluing styrene time here is your friend here,NOT your enemy.
The glue sets a chemical melting process that takes time to gas out.Whe it,s dry it is very strong.Check a spot easy to fill with putty with your fingernail.If it makes a dent the joint isn,t set yet .Give it another day and go listen some good music and have a lemonade and return tomorrow. GOOD LUCK TANKER-builder