I found that by using this method, i was able to mostly achieve my goal:
//Assuming in the RunWizard method of IWizard, the provided applicationObject parameter has
//been cast into a class field _dte of the type EnvDTE80.DTE2
Solution2 sln = (Solution2)this._dte.Solution;
if (sln != null)
{
Project folder = sln.AddSolutionFolder("Solution Items");
foreach(string name in [FileNamesToAdd])
{
folder.ProjectItems.AddFromFile(Path.Combine([SolutionFolderFromReplacements], name);
}
foreach (Document doc in this.Application.Documents)
{
if ([FileNamesToAdd].Contains(doc.Name))
doc.Close();
}
}
//This solution does not close any external editors for files added to solution