I'm wondering more about the startup time for the calibre server. If you turn off the automatic startup for the calibre server, does that have any effect on your startup time? On my laptop, it takes the startup time to 6.09 seconds which is not even close to your 2 minutes+ but I am not seeing the DEBUG httphelper and SMART_DEV lines.
Code:
Started up in 5.66 seconds with 7423 books
Started up in 6.09 seconds with 7423 books
The debug message around EpubMerge and the fanficfare_macmenuhack seems to show up rather often but I doubt that it is causing the long startup time.