Do them both while you are there. Police Certificate can only be done in person at a specific location in Lagos. You just show up, give them your ID, pay a bit of money (5,000 naira, I think?) and then come back to pick it up a couple of hours later. While we waited we went to the National Museum which is not far away.
As for medical, it can be done in Abuja or in Lagos, but will be cheaper in Lagos because there are 2 doctors and thus some competition.
One more idea for you...after we were married we went to the Canadian High Commission in Lagos (on Victoria Island, not far from the police headquarters) and paid for them to make a notarized copy of the certificate. Actually, we paid for 2. I can't remember for sure, but I think it was around $20 cdn per copy. I think this is very important for making sure your application goes smoothly. Someone else on this forum had to have his MC authenticated in Abuja before his interview in Accra, yet we were not asked to, and I wonder if it's because we sent a notarized copy from the Canadian High Commission.
Oh, I almost forgot! I found out about this later but wish I had known. When you're at the police headquarters, you can go to the passport office (not far away) and if you bring your passport and your marriage certificate, you will receive a special type of visa for Niger Wives. It costs nothing, and will allow you to travel to Nigeria without obtaining a visa. Basically a free 'mini citizenship' for women married to Nigerian men. It's valid for as long as your passport is valid.
All of that should keep you busy for a day!
Hope this helps. PM me if you have any other questions.
wow!!! thanks for all that info

very useful