I think I would go with 4.0
I do not think it will mess up your vs installation
I think when VS 2013 originally shipped it did ship with .NET 4, but apparently now in later versions (update 4) it ships with 4.5 instead
There are very good reasons why some projects in our solution target older frameworks. Until recently we supported 3.5, 4.0, and 4.5 .net and keeping the business and data layers using lower frameworks meant we did not need different versions of those layers, the same version worked with any of the web ui projects, only the web ui projects targeted higher frameworks 4 and 4.5
.NET is largely backward compatible so assemblies compiled against older frameworks can easily be deployed in newer hosting/runtime environments. When we say mojoPortal requires .NET 4.5, we mean it requires .NET 4.5 hosting, it doe snot mean every included assembly is compiled for 4.5. Whether all assemblies target 4.5 for compilation is a separate issue. Since we no longer support 3.5 or 4.0 we could change all our projects to target 4.5 but I have been reluctant to do that because I've wanted to keep it not too difficult for an expert to make their own build for older frameworks and there was no real need to change the target for the business and data layers. If I decide to do that for the next release of mojoPortal it will mean I also have to make corresponding compatibility releases for all of our add on products even though they have no new features, and anyone upgrading mojoPortal will have to upgrade those features at the same time, and the new version of those features won't be compatible with any previous version of mojoPortal, so that will be kind of a hassle and I'm not in a hurry to do it.
I recommend install the needed reference framework for VS.
You could conceivably change the build targets on all the projects in your local copy, but it has to be done in a correct sequence or you will lose project references in the process. Unless you are a super expert I don't recommend that.