That's pretty much par for the course....most dealerships will give you more of a discount on the stuff sitting on the lot than for a special order for several reasons. First, it costs them money to have these vehicles sitting around, and you do them a favor by driving it off. Second, they sometimes get a "holdback fee" to move cars by a certain date. When you special-order something, there is no guarantee what date it will arrive. Third, when you special-order something, your word may be good, but the dealer looks at it this way: If something unexpected happens....the financing falls through, or if it gets repossessed, or if you change your mind after a few months and trade it in ( trust me...it happens ), here they are stuck with a non-standard car built especially for you, and their reasoning is it may be hard to resell. Now, I don't necessarily agree with all of this reasoning myself, but this is traditionally how many dealerships work. But, to be honest, you are certainly not the only one out there looking for a 5-speed.
So, in a nutshell, don't be surprised that the dealer asks more for a special-order car. I had to pay a little more myself for my non-standard car....a yellow 2001 IS300 with cloth interior and without the sunroof (I'm too tall for it when it's closed...it cuts out too much headroom). They were hard to find. But it was worth it...it was EXACTLY what I wanted.
Good luck with it.