How much physical therapy have you done? Targeted stretching/strengthening/massage is usually necessary to get over tendonitis.
What is your bike fit like? Biking shouldn't aggravate the hamstrings so it's likely your seat is too high, far back or your cleats are off.
How many miles were in that week of fall running? Start off at really low mileage (like 5 mpw) and build from there. Big miles will aggravate old injuries.