Alfresco already includes some jquery version for one dashlet and the calendar view.You'd have to do some template overriding/patching to get in your new version - and then it might break those existing components. A customisation to resources.get.html.ftl web script like you did will only work with non-conflicting files / frameworks.
Generally, it is not recommended to bring in new frameworks or different versions into existing Share components unless Alfresco is not using them anywhere at all... Even within defauit Alfresco there are already conflicts (e.g. between TinyMCE bundled by Share and Aikau)
The Dojo JS file is included by the dojo-bootstrap.get.html.ftl included in the Surf library as part of the base page render. Technically you could configure the file via an override in share-config-custom.xml using the "WebFramework" config section and the dojo-pages > bootstrap-file XML element structure - though I would not recommend it as it could break the Aikau-based functionality.