I mainly do MTB, but did IM and a few of the half's and shorter tri's a couple of years back and had the same problem of not being able to find a comfortable setup with tri bars on my road bike, even with the seat all the way forward. I also found that the tri bars didn't get me much more aero than riding in the drops and that position also strained/fatigued my hip flexors despite doing quite a bit of core/flexibility work. So I was considering riding without the tri bars. Then I put on a Profile Design forward seatpost (entry level aluminium type that was only a few 100 R's at the time) and that made a huge difference to comfort when riding with tri bars (although it does look strange...). I also tried different stem length/angle/spacers to get the setup right. Obviously this is nowhere near as good or as fast as a proper TT bike, but I found it to be a good compromise that was far better than the standard road bike setup with tri bars. I'd recommend trying it, but also go to a bike/tri shop and get your setup checked.
