can you try adding this in Web.config inside the <pages><tagMapping>

<add tagType="System.Web.UI.ScriptManager" mappedTagType="AjaxControlToolkit.ToolkitScriptManager" />

and see if that solves it or not?

a request timeout can happen for a lot of reasons after config changes, I would try again and refresh if it times out to give it another chance in case it just timed out waiting for jit compilation to finish.

"Tried adding that code to the web.config file again, it refreshed the homepage this time, but when I tried to access a page with the form on, it errored."

ok, better back that out then.

I'm starting to think that the server must have a different version of ajaxcontroltoolkit installed in the GAC and somehow it is using that instead of the one in in the bin folder which is the correct version.

I really wish you could move this installation to .NET 4.5

The thing is your error says:

"The requested script resource 'Common.Common.js' requires version 'AjaxControlToolkit, Version=4.1.7.123"

and 4.1.7.123 is the version of AjaxControlToolkit.dll that is in your bin folder (or it should be since that is what is in the package)

so the question is how or why is it using a different version, and one theory is that there could be a different version of it in GAC (global assembly cache) on the server and somehow it is using that one instead of the one in the bin folder. This is just a theory about how this error can happen since I am not able to produce the error myself.  You could ask the host to look under Add/Remove Programs to see if it does have AjaxControlToolkit in the GAC on the server.

mojoportal and other features  like Form Wizard Pro do reference version 4.1.7.123 and it does exist in the bin folder, so it should use the one in the bin and it should not produce an error, so I'm just guessing at a scenario that could cause this error. I tried yesterday using the .NET 4 version of the dlls for mojoPortal and Form Wizard and was not able to get this error to happen.

The other thing to consider is whether you are really sure what version of .NET is installed on the server. It is actually not easy to find out without looking in Add/Remove Programs because .NET 4.5 is really an in place upgrade/service pak for .NET 4 and they both use the same version of the CLR. If you look under Administration > System Information in mojoPortal, it is going to say "v4.0.30319" no matter whether it is .NET 4 or .NET 4.5 installed, so don't let that be a basis for thinking it is only .NET 4 installed. .NET 4.5 has been out for 2 years now and it is like a service pak for .NET 4 so there is really no reason not to install 4.5. The .NET 4 package of mojoPortal can run on either 4 or 4.5, but the 4.5 package of mojoportal and add ons are compiled for 4.5, and the most recommended configuration is to use the .NET 4.5 framework and the 4.5 compiled packages of mooPortal and related features.

you might also test whether something about the skin is a factor, ie do you get the same problem if you use a newer skin like art42-wallpaper. for example make sure that the layout.master has ScriptManager

yes definitely