Can you double-check if the master pages that the templates are based on are on the right place? Also, have you turned on the "Rewrite user control Register tags for not working controls " option?
If these doesn't help, then I suppose you have bad HTML on the master page, but you will have to send it, so we can check it here.
Another thing that I can suggest is to apply for our holiday upgrade contest:
I believe my colleague Miroslava has informed you that you have been approved for our migration event, so your issue will be solved by our upgrading team. Can we close this ticket now, so that you can continue your communication with Miroslava?
Is there a chance that you could open a support ticket, so that we can discuss the problem and see how we can help you with the migration there?
All the available documentation on migration can be found here:
Actually, as far as I understand, your migration successfully passed, is that correct? The old APIs however, are not backward compatible, as this is not an update, but a migration to a "different" CMS (it is working in a completely different way). Having said this, your code will need to be replaced with the new APIs, which can be found in our documentation and also all references to old assemblies should be removed and you need to use only the new ones. For an examples of working with pages, here's the section that you can refer to: