Unless you know that the boat has had a severe close encounter with some under water object, I would doubt very much that your keel bolts are loose. Closely inspect the keel for signs of damage. If they need tightening, I''m sure the manufacturer can give you the correct torque specifications. You might also want to check the bilge in the area of the weep to make sure some dumbshit didn''t drill a hole in the boat while working on or replacing the bilge pump.
Break out all of the loose faring material around weeping icon and let it dry out over the winter and fare it prior to bottom painting in the spring. I''ve used a two-part filler called VC watertite in the past, there may be something better, don''t use Bondo or auto body filler as it is not designed for underwater applications.
To replace the cutlass bearing you''ll need to remove the propeller, most likely with a puller. A special tool is now available to press the bearing out of the strut obviating the need to pull the shaft. I paid the yard to do this a few years back, about $130. The cost of the tool and the value of my time made this an easy decision. Don''t forget to spray the new bearing with oil (not sailkote) at time of haul out next year, to keep the rubber soft, flexible and prevent it from drying out.
Engine alignment should only be done once the boat is in the water and the standing rigging is under tension. Unless you have very good mechanical abilities and a good dial indicator, hire a pro to do this, you can do more damage that will cost you a lot more down the (water?) road if it''s not done correctly.
Any chandlery can recommend a good flax (Teflon or otherwise) to repack the stuffing box. This is not a big job but, you''ll want to make sure the box is adjusted correctly so you don''t burn up the shaft or sink the boat in the spring. You might consider throwing away the OE stuffing box and replacing it with a drip free stuffing box from a company such as PYI. I helped a friend of mine install one on his C30 in about an hour.