Nice, large bike budget that you have.
I'm a newbie, but my sister has officially given me the title of "bike nerd".
So, my personal opinion is that if you are a very flexible, athletic person that does not have any funky anatomy and if you have tried riding all the brands of bikes that you are interested in and they all fit, then you probably do NOT need to go custom. Get that Ultegra Di2 that you are drooling over along with the better wheelset instead of the Custom bike with lower grade components. Also, since the 2013 are in, a lot of LBS are selling their 2011-2012 bikes at a discount
Big warning....I am a newbie. But I still want to see a bike photo to celebrate with you when you decide.
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2012 Specialized Amira Elite, upgraded carbon handle bars, Jett saddle 143mm switched to 145mm 2012 Selle Italia Max SLR Gel Flow saddle
2011 Specialized Ariel Sport,suspension post,Serfas Rx Women's Microfiber saddle