Hi Andrew. Are you experiencing any discomfort on the trainer or do you feel like there is a loss of power, or a noticeable difference in any aspect of the pedal stroke when compared to the road bike? I'm a bike fitter in Australia. While it is ideal for indoor and outdoor bike setup to be identical IF you want the indoor bike to feel exactly the same as the outdoor bike, it's otherwise not essential. If the difference in crank length isn't causing you any issues then don't worry about it. What's important is that your saddle height, saddle setback from BB and reach to the bars/hoods are the same as your road bike as a starting point. If you measure saddle height from the pedals it should be the same as the road bike. If you measure from centre of the BB then remember to account for the 2.5mm shorter crank by raising the saddle 2.5mm when compared to the road bike. 2.5mm isn't much, but if I was being pedantic, saddle setback (saddle back by up to 2.5mm) OR cleat position (cleats back by up to 2.5mm) may be appropriate. That will maintain the same amount of knee flexion in the 3 o'clock position during the power phase of the pedal stroke. I wouldn't bother unless you feel that you are tipping forward when pedalling with the shorter cranks. At the 9 o'clock position during the pedal stroke there will be less knee flexion with the above changes, but being a lightly loaded phase of the pedal stroke you might not even notice.

As Gary suggested, it would be very useful if you could video yourself riding, especially from both sides. Saddle height may be something that needs to be adjusted. What length are the cranks? the length will be stamped on the inside of the crank arm. A photo of your shoes showing the cleats from multiple angles would be useful as well.

@Pete Smith I've used the Favero Assioma Duo Shi for about three years and love them. Unfortunately, I don't think Favero make them anymore. They have since released the Assioma Pro RS, which comes complete with SPD SL compatible pedal, but only in a normal SDP SL 53mm axle length. I bought the Duo Shi because I wanted both a pedal-based power meter and a wider stance width so it was the perfect solution. These days you'd need to use cleat extender plates like those from FORM Bikefitting to get 10mm of lateral adjustment. Plus or minus whatever lateral adjustment you can get out of moving the cleat. As far as I am aware, you can't use washers between the crank arm and power pedal to increase stance width as it will affect the accuracy of the strain gauge. It will be calibrated to a predetermined amount of flex in the pedal axle and wouldn't account for the small amount of movement that may occur with a washers.

I'd love to attend, but that's 1am for me in Australia. If there's ever a variation in time I'll try to make it.

@Andrew Hughes "level" is different for many saddles and depends on the saddle shape front to rear. So the model of saddle and how you measure saddle tilt will determine what "level" looks like. How much, if any, saddle tilt (nose up or down) you might prefer can be influenced by how much you rotate your pelvis on the saddle. Generally, a more aggressive riding position with a lot of saddle to bar drop will require more anterior (forward) rotation of the pelvis. This may, depending on saddle shape, require a more nose down setting than a less aggressive riding position. SQlab and ISM saddles, for example, tell you on the packaging what "level" looks like. Some manufacturers have really good info on their websites for setting saddle angle. How did you measure the angle on your saddle and what brand and model is it?