Only possible problem I could see here is - is your one way valve dead centre (and in front of the outboard? if so you'll need to drill a new hole. It won't be a problem - the hole is drilled right down at the join with the deck You could could in theory hold the transom to the floor with a piano hinge (structurally, I'm not taking watertightness into account here!) My boat has two 70mm holes, and the transom's as solid as the day it was built (and that wasn't yesterday!) As a thought, if you do need to re- site it, if you are careful, you could use the 70mm Core as a plug for the 50mm hole you are filling in. Alternatively, just leave the 50mm alone & put one of those compressive bungs in it It is more likely to help drainage out the water, as trunks tend to fold & seal themselves.
As for the draw cord, that will depend on a) how easy you want access b) how often you plan on using it. There is a thread on here about it. Standard trick is a jam cleat on the inside of the transom. I've led mine forward and use a bit of bungee to make sure it drops when i release it - means i can raise / lower them from the helm position. if you take this option, the actual cord route will depend on your boat's setup.