I've just played this game for exactly that reason. Trust me that will be a very big hole buy the time you get rid of all the shite metal off.
The best thing to do is weld a new formed plate over the hole, you have to get rid of all the rust and knock it back to good steel, thats why the hole will get bigger. As you have the pipes off may as well weld another plate over the 2 joins of the collector box, where the four go into two and the two into one. If you can weld great, if not get a professional as it is thin steel and you may blow a hole in the good pipe, £50 it cost me to get that done.
New gaskets are best, but if yours are the crushed copper ones you can heat them up and then drop them in cold water, not done it myself but its meant to work.
There wont be any hole in the downpipes before the silencer/end can, other wise it wouldn't be silenced. There is a small drain hole at lowest point of the silencer in the stainless steel.
Any VHT paint will work, don't worry about perfection when spraying it on, most of mine flaked off after a month in this weather.
Good luck