I am sorry of I created a poor impression of the Moodle-Windows interoperability, that was not really my intent, but it is something you need to be cognizant of when making decisions about how you are going to approach the entire issue. I cannot agree here though,
"Moodle and all its add ons, does not play well with windows"
I don't think Windows plays well with anything that is not part of the Microsoft environment. I had one Tech tell me that with Windows 7, the ONLY programs he has installed the way it is supposed to has been the Adobe products nothing else has. His mirrors have all had to be rebuilt and he does not understand why - he is frustrated as he has never had that happen before. It appears if Microsoft does not set a standard that a program uses, it plays havoc with that program. This was part of the issue with the anti-trust suit against Microsoft years ago, that they got out from under. The Judge found they were wilfully refusing to provide other developers with sufficient information to be able to construct programs that essentially competed against Microsoft products to enable those developers to have software ready to go when a new version of Windows was released. This is the same thing that Boeing did in the 1950s with their jet engines and air frames. The Judge made a mess of it and instead of trying to create a similiar situation that Boeing has now, the engine is sequestered and everyone gets the same information at the same time, he tried to create a Baby Bells situation, a mistake. Microsoft appealed and the States ran out of money, so the case died and Microsoft got its monopoly.
Consider Moodle, it was developed under a non-Microsoft set of standards, it does what it does well, and it can run in any environment. I have four test Moodles on my XP box, and do things in them that I need to do. I have used them to test issues in the production sites I have worked on. I am actually a contracted teacher so I am not let too loose on servers, but the servers I have worked on have been one Windows 2003 Server and two Linux servers. (Currently I am Admin in two Moodles but one of those will end soon, and as I am no longer associated with that environment, at my suggestion it won't be renewed, and it suits me for lots of reasons.)
Moodle runs well on Mac OSX and all flavours of Linux. It also runs in both Apache and IIS, but there is some additional tweaking in IIS not required in Apache. You can use Bitnami to install on Windows 7, or run it in a Xampp environment but I think there is some issues there installing Xampp, the Xampp site should have more information. In short, Moodle runs anywhere, but in Windows, there is required additional tweaking and administrivia that is not required elsewhere. I am just too lazy to jump through all those hoops and I resent the neccessity for doing so. I should not have to. I can turn all the "security" nonsense off, I am sure, but I got more important things to do than to spend the time doing it.The things I do in my XP box I then either copy to the production site or upload using an FTP program or create new courses and backup/restore from my Moodle. If it is an issue with some Moodle code, I use the test site to ensure it works then replace entire folders on the Production site, if necessary (not often). Moodle does not change, it is a "write once/run anywhere" tool and is usually easily repaired if something fails.
Seriously suggest that what you do is to set up your test Moodle on your private machine, use Bitnami to do so. Add in the Maths tools MathJax, Geogebra, AsciiMath and whatever else you feel you need. These forums will give you a lot of ideas of how to do that. Once you have that sorted, begin to develop for your production site. But bear this in mind, resources can be found anywhere on the Web, it is the activities you give your students that are the really interesting thing for them or not. I am changing a lot of my strategies to "go here - think about this - use this example as reference - do this activity" particularly for Maths and increasingly for science. Not sure if it is working yet, but will see, time will tell, and then there are equity issues for those of my students who do not have a computer at home, or who do not have internet access or so on. However, I am thinking it is a better approach, engagement through shared experience and mutual support rather than a lecture or similar class work...