running dilema

I finished my triathlon season (2 sprints and a oly) and am now into my marathon training for Marine Corps at the end of October.  This will be my second Marathon and my background is in running.  I have previously never had any issue with running or injuries but I have found that my long runs (16 last week) have really set me back.  I've been having lots of "pain in my butt"  or where my hamstring tendons attatch at my ishial tuberosities (sp?)

My program calls for 3 runs during the week (one usually temp or drill/speed) and then the long run on the weekend.  I've noticed that I really need 2 or 3 days after the long run to feel better and not be in pain.  Im torn between whether I should cut out a weekday run and do a swim or shorten the long runs for the next two weeks or so ensuring that I get the 4 days of running in.  Quality vs quantity I guess. 

Any thoughts?  Anyone have a "pain in their but" before?  I've been trying to add yoga to help with the stretching but the pain still remains for at least 3 days after a long run.  

Thanks in advance