Everything has been received and stored as you said, visual manifests are preferred but be sure to report each delivery in some way. You may consider the Plutonium and Hazmat deliveries completed, but if one transport wishes to 'top up' any additional commodities, they can be paid for it as well.
As for the timings, I will give you a two-week extension to the 6th of May for the transport captains' bonuses, paid at the end of the contract.
When we came to Coronado, there was of course a significant... unaffiliated presence. Rather than stir things up (ask the Guild about that), they are generally left to do their business in the cloud if they don't cause trouble. However, Sabah and it's defences will keep themselves safe as a precaution. This can easily be fixed by having a word with some members of the Guild, or perhaps helping with their bounty work.
Keep up the good work, and maintain your high standard of safety.