Is your application under express entry or spousal application??
You have no issues if you submitted at Accra, Abuja is not collecting passport from for now
A Ghananian friend visited the embassy and confirmed it, CIC recently added AVO among the embassies that have open for work. I would have send the link but I think is against the rule here, you can google it
You just started, medical request will be in July. So i will only advice you to book for medical ahead of time.. You can book for July 12, you will get medical request on or before the date.