The includes should not greatly slow down your site so much that you are noticing it.
A browser doesn't even know that a page started in 2 or more pieces. The server reads your request from the browser, pulls this PHP page and sends it to the PHP interpreter. The interpreter sees the includes, packages them in to the page, and sends that to the browser.
So if your page is loading, just slowly, then its not the includes, since the page is sent to the browser as 1 piece, not as 2 or 3.
If the includes were slowing it down there would be a delay in getting a response from the server, the same with anything serverside, like DB queries and the like.
So look for other culprits as to why your page is loading slowly, perhaps images or tables.