Bike fit / correct riding position

Thanks for replying Scherrit - I've been cycling for about 9 years now and this issue first came about 2 years ago. I've never had hamstring issues before, but have suffered from acute achilles pain (right leg) when cycling and hip-flexor pain (both sides) when trying to up my distance too quickly during running...
When this issue first arose in 2012, I was probably running more than I was cycling. I bought a new bike in 2011 and I haven't changed my shoes, pedals (or even cleats) since then.
I've never had hamstring problems before and when running there is no pain whatsoever (execpt maybe after the ride in a Tri).
At the moment I am mixing the week up with a short (1hr max) fast bike session and with a ~3hr 15-16mph ride on the weekend in the attempt to work on overall condition.

Boring update - Put my track bike together and went out for a fast spin on it for the first time in a couple of years. No pain at all.
So I attempted to mirror the fit of it onto my road bike. Installed 15mm extra spacers under the stem and raised the saddle 10mm, which has really helped. Moderate paced 50km yesterday with only mild discomfort after ~30km.