The coil can break down due to heat and quit working. The coil will then cool down and work just fine for awhile. It is common and usually happens after the motor runs for awhile. Most Atomic 4's have the coil mounted to the block and this is where the heat comes from. One trick is to mount the new coil on a bulkhead close to the engine. Keeps the coil cool. This trick comes form people using electronic ign. which causes the coils to get real hot.
As to the packing, I am not a fan to those hi-tech shaft seals. If you just mess around in local water I guess they are ok. But if you are a cruiser and one breaks, (they do break) you can't fix them and you will have water gushing into your boat. With the goos old stuffing box you can repair them with just about anything, rags, shoe lase, etc.
To replace the packing you can do it in the water or out, It's your choice. In the water you will get wet but not so as to sink the boat.
Here you go for the in the water fix.
I have an old bicycle tube that I have cut to make a long wide rubber strip. Rags will work also.
1: Get the right sized packing material for your shaft/packing nut. I use the teflon impregnated type.
2: Cut three pieces of the packing, so each piece will fit around the shaft. make sure to cut the ends of each piece on a diagonal. Dont cut the ends square.
3: loosen and back off the jam nut. That is the thin nut just behind the big packing nut.
4: Now back off the large packing gland. Grab the big rubberband that you made and wrap the shaft so the water stops comming in or slows to a trickle. You got wet didn't you?
Stop and dry off and let your heart slow down a bit, Wipe the sweat off you.
A jigger or two of Pussers fine rum will help. Perhaps this should be step 1
5: This is the hard part: You have to get all the old packing out. Sheet rock screws work alond with dental picks or an old small screw driver with the tip bent over to form a hook. Another hit of the Pusser's would be helpful here also.
6: Wrap the 3 pieces of packing around the shaft, inside the packing nut. Making sure you have the joint of the pieces of packing staggered.
7: At the same time remove the innertube rubberband and skide the packing nut back and thread it back on. Back the nut just until the water stops driping. Run the jamb nut back and lock the packing nut.
8: Get another hit of the Pusser, fine rum and fire the engine, put her in gear and let it run a bit in gear. Watch the stuffing box adn see if there is about 2 drips a second. Shut her down and feel the stuffing with your hand. It should not be hot to the touch. If is is back off on the nut just a little. Note: It will be warm but not hot.
9: Sit back, pour the rest of the Pusser's and congratulate yourself for a job well done.