Hi Neil,
Regarding the shopping cart not clearing - are you by any chance using any type of maintenance plugin? If so please deactivate it because this has been known to cause such behaviour.
Regarding the absence of download link on the thankyou page - can you please double check that you have the following shortcode on the thankyou page:
[wp_eStore_transaction_result:end]
In addition, please see the following video which explains how to set up download link and follow it's instructions from scratch:
http://www.tipsandtricks-hq.com/ecommerce/wp-estore-instant-digital-product-delivery-499
Also, can you send a link to your thankyou (or return URL) page?
I've looked at your debug file and the logs show that the purchase was correctly processed and the download link was identified so we need to check if there's something on that page preventing the shortcode from working properly.