I bought all new gudgeon screws from Hobie. Its a small expense. I also tapped out the holes to clean up the threads (#12-28 I think) and used 3M 5200 since these are hull penetrations below the waterline. (At the time Loctite did not make any marine products.) Your biggest task will be getting the old screws out especially if the boat has spent any time in salt water. Might want to have some easy-outs on hand. The heads strip out pretty easily and sometimes even break off.
That's a bit of overkill.
Don't use 5200 if you ever want to get something apart again. 5200 = forever stuck together.
You can re-use the machine screws. A 2007 boat shouldn't be corroded tight (mine certainly isn't, but I sail mostly in fresh water).
Use a bit of regular silicone seal around each screw. Periodically check the screws to make sure they aren't loose. Go sailing!