I think you do not have a good project definition here. For every (or almost every) product on Windows platform there will be functionally similar (sometimes better, sometimes worse, sometimes just different). You can replace what you have with new software and then the thing will come crashing down around you.
Deployment of products providing functionalities you want is easy. It may be, depending on a scale of the thing, a huge, time consuming project and take months to complete, but it is not a big challenge.
The much bigger problem will be integration of the whole thing, to make different parts cooperate and understand each other (e.g. single sign on).
Then there will be even bigger issue: you are a Microsoft shop, and suddenly you'll need Linux administrators. If you want to do the infrastructure migration internally, then your ability to do business will perform of the ability of your new Linux administrators to do their work. Apart of that you will need to train your users. If you change anything end-user facing, the users will need to be trained. The fact that your new solution is functionally superior to Sharepoint will not prevent your users complaining, that the thing does not work. Faced with different menus they will have problems.
If you plan to switch to Linux infrastructure as an offering for your clients, then again you need to bring the expertise internally. Otherwise you won't deliver quality products.
Yes, you can replace Windows infrastructure with Linux one. You can support it and have your users use and like it, but it is a huge undertaking.
