TEMPLATE NOT FOUND issue due to non access of field in email Templates. Salesforce is saying that Email Template is using standard controller even for Visualforce templates using without sharing classes. So you can't send email through template if user don't have access of fields used in template!

Send email from Apex is counting against limit of email send so its necessary to send email through email template by workflow. We tried a work around and its working fine. Follow following steps:

1. Make a field on object from where email need to send.
2. Make a workflow that send email on change of above field you made.
3. Use email template that contains above made field in template.
4. Populate field when condition matched or need to send email.