OSX 10.9.5 start up takes several minutes to connect to internet

My mac mini has now got a faster boot up time since having a SSD installed.  However, I have noticed it takes several minutes for it to connect to the internet.  Under Login Items, I use to have my NAS setup to connect a drive on start up.  But, I always received the error "There was a problem connecting to server."  I removed it.
What I have tried so far:
Upgraded from 10.8.5 to 10.9.5, that didn't change anything.
I have a Airport Extreme router (7.6.4) and even swapped it out for a Linksys router to see if that was the issue.  That didn't matter.
All new ethernet cables for the router and mac mini.
Firewall turned off on OSX.  I have since turned it back on since that didn't change anything.  I do have Little Snitch running too.
Any other suggestions would be greatly appreciated.

Welcome to the Apple discussions.
When you say your machine is near capacity ... you want to keep at least 10% of your hard drive empty for systems usage. Less than that and the system slows way down.
One thing you can do is to use this tool to see what your largest files are on your system - move data to an external hard drive and delete, or just delete unused/un-needed data: http://software.filefactory.com/Mac/WhatSize_10-3-91.html
You might also run MacJanitor to run the daily/weekly/monthly scripts, which sometimes don't run automatically: http://personalpages.tds.net/~brian_hill/macjanitor.html. Some have found using a utility like OnyX can help with disk space. OnyX is available from http://www.titanium.free.fr/pgs2/english/download.html . Note OnyX does the same thing MacJanitor does, plus much more.
You can use Monolingual to delete the languages you know you'll never use from the operating system - depending on choices it can save over 1GB. Choose language options carefully, as you can muck things up if you rush through it: http://monolingual.sourceforge.net/
This FAQ is good reading on maximizing disk space: http://www.thexlab.com/faqs/freeingspace.html

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