I've made a bit of a mistake

I got things running and noticed the timing chain was making a racket.
I had forgotten to remove the 2 bolts under the crank gear and replace with countersunk screws.
I'm going to replace the chain and rectify the bolts.
Three questions:
How do I countersink the holes? The engine is in the car and the front panel is on. I'm not sure how I can get a drill bit in to open them out as there is not much space?
Is it worth buying a full duplex kit or just the new chain and screws?
Do I need to modify the ital timing case any further (the breather canister has already been modified)
Thanks
Tom