Resolved Lag Spikes

I'm having lag problems, but only in certain situations. Whenever I get near a generated structure or am near the center of my custom ship (or a regular ship), the game has lag spikes. It freezes for a second, drops by 10 to 15 fps, crawls back up to about 30 fps, then freezes and drops again. It only started doing this one morning, it was working fine the day before with no lag. This doesn't happen near anything I've built on planets, or in the wilderness on planets.

Operating System: OS X 10.9.5
Processor: 2.4 GHz Intel Core i5
Memory: 4 GB, 1333 MHz DDR3
Graphics: Intel HD Graphics 3000, 384 MB VRAM

Mods:
• WEdit - World Edit Tech
• MadTulips Spaceship Mod
• Modules in a box (Dependency)
• Manipulated UI
• Spawnable Item Pack
• CrazyFreak's Musical Collection
• (TanzLO) Dark Player Aura
• (TanzLO) No passthrough
• Extra Zoom Levels
• Extended Songbook
• Purchasable Pets

 

I've edited my original post, it should have the correct log file now.

I'm not sure about the ram usage, but the cpu usage increases by a large amount whenever I experience the lag.
The only other software running besides starbound is Steam.

UPDATE: I loaded another character, and the lag spikes still happen, but they're so small that they're not even noticeable. I only realized they were still happening because the render fps was dropping and then returning to normal in the same way as the problem character, but with a much smaller drop. I don't think it's a problem with the custom ship, because this new character I loaded has an even larger ship.

UPDATE 2: I transferred the problem ship on to this other character and it started having problems, so it definitely seems to be a problem with either something on the ship or the ship itself, not the character. I just uninstalled all of my mods and the problem went away, I'll try re-installing them one by one to find out which one caused it.

UPDATE 3: I think it was MadTulip's Spaceship Mod causing the problem, when I uninstalled it the lag spikes went away.