Barbara has it spot on. You have to think about the fact you're running a business, and that you need to make sure you have that profit. There is no guarantee the items will sell at a lower price, and they are going to be the things enticing people into your shop and bringing in those custom orders. If you try to get rid of the things enticing people in, you may find that you get reduced traffic and fewer of those custom orders!
With regards to some of your stock, they are the sort of things that people are likely to want to customise- I have those in my shop as well, so there are a few made-to-order items as well as ready to ship.
Having a good selection of ready to ship and custom items is always a plus to cater for the people that have planned ahead and the people that want off the shelf stuff!