Like others have said, Thomas you can adapt yoga as you wish, however, yoga is not going to adapt for you. The fact of the matter is yoga is a complete philosophy and practice, and teachers of yoga are going to cover it all, otherwise it would not be teaching complete yoga. To expect them to filter out some stuff to respect your religious sensiblities is unreasonable, because ultimately it is your choice whether you do yoga or not and your choice how many of its practices you want to do.
I am not going to attempt to convince you about chakras, nadis, kundalini etc, but it should be known this is the science behind yoga and why it works according to the yogis. There is no doubt about yoga working, it obviously works very well, but why it works so well cannot be explained using just a purely physical approach, one has to look at the claimed subtle dynamics that the yogis have mapped out.
I personally think it is a bit disrespectful to reject the theory behind Yoga because this is undermining the investigations done by the yogis over several millenia and the data they have collated over time. It is akin to rejecting the research of an entire culture and this is a very ignorant attitude, in my opinion. Especially when the technology of yoga they have developed works so well. If the practice is sound, the theory it is based on must also be sound.
In any case yoga does not require you to begin with any beliefs in the theory. Theory is not knowledge itself, it is just possible knowledge. It only becomes real knowledge when it is experienced. So just do the practices and find out for yourself whether the theory is right or not
You can construct your yoga program as you wish, there are no fixed ways of constructing a yoga program. However, some programs are obviously more effective than others and the chances are if you devise your own, it will be as effective as the ones devised by experts. Generally, and just some helpful advice, you will stand to benefit much more from yoga if you practice all of its aspects.