How can I open a file in Pages that does not have an index.xml file?

You have two versions of Pages installed. No release of Pages v5 contains the internal Pages '09 index.xml file. If Pages '09 is presently running, and you double-click a Pages v5 document, Pages '09 will present the missing index.xml file dialog.

Quit Pages '09, and then double-click on the Pages v5 document. It will open correctly in Pages v5(.5.3).

Laura,

Pages '09 has 100+ more features than Pages v5.5.3 on Yosemite — because Apple wrote Pages v5 entirely from scratch. If you want to work productively without wondering where this or that capability went in Pages v5.5.3, then I strongly recommend NOT removing Pages '09 from your Mac, and making it your primary word processing application.

You are fine on Yosemite with Pages '09 v4.3. You just need to remember that with Pages v5.5.3 and Pages '09 installed, the default application launched by a double-click on a .pages icon will always be Pages v5.5.3, and otherwise, Pages v5.5.3 documents are not backwards compatible with Pages '09 without first, exporting them to Pages '09.

Historically, I have recommended that for mixed Pages environments, that users place blue and yellow tags on Pages '09 and Pages v5 files respectively. At minimum, a yellow tag on Pages v5 documents. Visually, this will prevent you from opening a Pages v5 document in Pages '09. When exporting a yellow tagged Pages v5 document as a Pages '09 document format, you will have to change the filename to avoid an overwrite of the Pages v5 document, and change the yellow tag to a blue tag prior to selecting the export button.

In Spotlight, you can tell it to find all Pages documents with blue tags using this string: (tag:blue kind:Pages)