Hey Craig,
A good once over the whole helicopter is never a bad idea but to me some key points would be check over the tail belt (since this is an N5c) and see if you notice any signs of wear and tear. Remove the main blades and slowly turn the head by hand, see if you feel any notches in the bearings of the main shaft blocks. If the belt needs replaced, do it but whether you need a new belt or not, coat it down with silicone spray just like you would during the flying season to keep it from drying or cracking.
Look over your main gear for wear and tear and especially all servo wires; In particular any place they come in contact with the frame, where they come out of the servos, and where they go into the plug ends. Pull the motor and check the clutch for life left and to make sure it's still seating and solid in the clutch bell. Finally, make sure to check all your plastic links for any cracking or stress marks. A light coat of tri-flow or other light oil on the main shaft and tail shaft for maintenance and storage is never a bad idea. You can always wait until next season but it's advisable to replace your fuel tubing every season or at least check it over with a fine tooth comb if you didn't put a ton of flights on the tubing the previous season.
If you really want to dive in deep, you can disassemble the main and tail grips and pull everything apart around the shafts there and with your fingers check for notches in the bearings, this would give you a more certain and in depth look at the health of your bearings. Grease up the thrust bearings again as well.
In regards to muffler sealing, I don't do anything special except put one of those metal end caps with the o-ring gasket in the exhaust deflector and clamp the carb inlet fuel tube closed. Now granted I store my N5c in the main part of my house with controlled temperatures but I have yet to have rust in my motor doing it this way.
Hope this helps!
Regards,
Brandon Bartolomucci
Sent from my iPhone