The diagram you showed is fine. That is really all you need to do. I might add a small strip of 1X2 along the wall as a nailer for the soffit. The only alternative would be substituting a vented soffit panel for the solid soffit. Using a vented soffit would help a little in exiting hot air and give a bit of ventilation. Best used with a ridge vent for really good ventilation, but better than nothing if used alone.
The plywood of your roof is typically not as thick as your standard galvanized steel roofing nail, so it is expected for nails to show through this in your attic. The plywood can and is expected to take a bit of damage over time and this is okay as long as the shingle has something firm to hold itself down onto.
Over time if the plywood is too damaged to properly hold down new shingles or becomes too dangerous to walk on safely then a roofer should be able to identify such compromised plywood board and replace it as needed.
What is worrying about your question is that you specified that the roofing nails have split and damaged the roof trusses. Standard roofing nails should not be long or thick enough to split or crack structurally sound dimensional lumber.
If this is what happened then you may have a problem unrelated to the quality of the roofing job. Your home is over 50 years old in a warm wet climate, so you should inspect for a number of different problems.
Dryrot
Termites
Carpenter Ants
If you have any of the following indications of current or past damage to any of the three items then that would explain split, cracked or damaged roof trusses during a typical roofing job.
On another note: The soffit typically fits into a groove that is known as J Channel when installed on a roof overhang. The roof overhang is typically MUCH too tall for any roofing nails to reach soffit. I imagine instead you might be seeing a roofing nails perforating the fascia, which can be a sign of a sloppy rushed job. Without pictures though we can't tell that for sure.
Best Answer
All roofing manufacturers require a certain size fastener (manual or pneumatic) shank size and head size. They also specify the minimum thickness of roof sheathing. This is primarily to resist wind blow off.
Depending on where the installation is located, the minimum thickness of sheathing is either 1/2” or 5/8” (for high wind areas).
You can buy the correct size (shank diameter and head size) and specify “shorts” (1” long) so they don’t penetrate the decking. These “shorts” exceed the roofing manufacturers minimum penetration.
If you use the wrong size fastener, you’ll void the warranty.