Tri bike geometry places the saddle way forward, compared to a tour bike. Many tri people slide their saddle all the way forward, on top of that. Then, many of them ride even further forward on the nose of the saddle. This maximizes usage of the hamstrings and glutes. Yes, it's primarily to save the quads for the run. But, many of these people are putting out huge watts for 112 miles at time. Reading many training logs, you'll find these competitors regularly putting in as many as 170 miles, on their training rides, on their tri bikes, multiple times per week.
Having a forward seating position does not hurt knees, too low of seat height will. As one slides the seat forward, the distance to the bottom bracket is reduced. So, a seat height adjustment will be in order.
Like "whittierider", I run my seat all the way forward. This rotates the hips up under your body and allows your weight to rest on your sit bones. Having a bike stretched out causes you to ride on your perrineal region-not good.
I'd still suggest working off the components already on the bike. Utilize the adjustments and try different positions. Throwing parts at the bike without experimenting with what you've already got just leads to further confusion.