James, you have indeed put up a very good solution to combat the slow speed of your computer. As you say, I think it will be a short term fix but please post back here if the problem occurs again. Once again, congratulations for fixing your problem for now.
As for your question regarding a Trojan, it will not activate itself unless you execute it. Trojans can be removed by deleting them but some of the more stubborn ones need advanced measures to remove them. Deleting the Trojan from your external drive should have removed it unless it replicated itself. However, please continue with the scan for safety purposes.
Once again, Thank you for posting your experience here. It may help us tackle future cases similar to yours.
-- Goku