This is clutching at straws, but is it maybe to do with the size of Meteor’s bundler cache? There have been reports over the years of this causing longer build times as it grows. In your application root:
rm -rf .meteor/local/bundler-cache
It may also be worth removing Meteor’s package cache from your home directory:
rm -rf ~/.meteor/packages/meteor-tool
The only reason I suggest this is that I’ve seen issues on the forums to do with open file limits on Macs (which could potentially affect Linux too). I don’t have a Mac and have not experienced this on Linux, so feel free to ignore me! 