My two cents suggestion
1. PCC - It is possible to do this when you physically absent and i suggest you do follow this route. I had same experience at the initial stage of my application. My wife was out of the country for a long period while i was in Nigeria and i needed to process her pcc. She simply printed the pcc form from the online site (http://www.nigeriacrb.com/apply_now.htm), completed the form, thumb printed it following the example provided on the site, and sent it to me in Nigeria via courier. I had it processed under a day (offcourse at a cost higher than the normal price). You can have someone process it this way immediately and courier it so you can quickly send to accra.
2. Medicals: i suggest you do this at your current location using a hospital/clinic from the CIC approved list for your current location.(see link http://www.cic.gc.ca/pp-md/pp-list.aspx). I Had same experience. My wife was out of the country and as a result she did her medicals in that location while we did ours in Nigeria and followed up with an email to accra explaining the situation. On the pregnancy, you simply need to inform the doctor at the hospital and they will conduct the chest xray while protecting your baby. I want to believe that other experienced members in this forum who have done their medicals while pregnant can attest to this and shed more light.
In my opinion, it is better to send in partly completed documentation and explain the situation to accra than not doing anyone at all. A colleague had a near similar challenge but went ahead to do some of it and sent an email to accra explaining the delay due to long timeline in processing his pcc from the USA along with his documented evidence showing his application for the pcc. Accra responded and gave him an exception to extend his deadline till when he gets his pcc. So on this basis, i will suggest you act swiftly because you have already lost two weeks of your deadline.
I leave it to other experienced members to add or remove....
Wishing you the best.