Hey,
getting a Tajik visa in Tashkent is a bit of a drama - it took us 11 days all up. Keep in mind however that everyone has a different experience- just depends if you get lucky or not. The scenes of locals at the gate in the morning is like some mob scene in a movie, and you have to fight your way through to the front. I'd recommend you go the travel agency and if you have the $$, pay them to do it for you. I overheard an American couple talking to their agent, and she said it would be ready in 3-4 days.
We went to the Fan Mountains and had fun while we waited, and hoped to zoom back to Dushanbe and take off to the Pamirs that day. We were told to return the following morning, which added yet another 1.5 days to the experience!
If you can, get the Tajik embassy to organise your GBAO permit at the same time - as getting it in Dushanbe is almost the same hideous experience as getting a visa!! If you're not Aussie (like us - we had no choice but to get our visas along the way as we have no embassies here) - I'd heartily recommend you get the Tajik visas - in fact all Central Asian visas - from your home country.
Of course if time is no problem then you should be fine!!