That's what Puppet, Chef, package management and a host of other tools such as virtual machine images and unattended installs are for.
> There's always some hardware that doesn't install correctly
Most server-grade hardware you buy from reputable sources is exquisitely Linux-compatible. I never had any problem with that.
> it takes an odd sequence of commands that needs to be run in just the right order to get things going
This indicates you are deploying servers without really understanding what you are doing. Your phrase evokes a series of spells that have to be cast in order to conjure the proper demons. Unix machines simply don't work like that - there is no magic.
> Invariably I waste hours on the internet searching forums every time I do this
Buy a good book, read and understand the documentation of the software you use. Hire an experienced consultant to teach you and your team, if needed.
When you understand what you are doing, it is really easy. Every piece is open to inspection and all you need to do is look inside.
> I find IIS 7 to be much easier to set up and customize than Apache in terms of hosting web applications.
Until you need to do something the GUI doesn't allow you to do.
> I also find it's much easier to administrate large groups of Windows servers because of the nice tooling
The tooling is there - you just need to learn it. We use Puppet where I work and we use it to manage our server fleet. Works as intended.