For a simple amp like this the two ground system (plus one safety ground) is a good system like you mentioned Morgan.
One ground point for low current ground's - preamp
One ground point for high current grounds - output section, PSU
I'd leave the input jack un-isolated that's fine for this low gain amp. However I would not use the input jack as a ground point like it is currently. The jack is going to come loose over time as you plug and unplug your instrument in hundreds of times. As the jack loosens the ground connection becomes compromised and then problems will just come poping up. In general it is never good to use a mechanical part as a ground connection or count on it being stable and lasting.
So what I'd do (and many other amps do) is put a little #4 hole an inch or so away from the input jack and have a terminal lug there for preamp ground connections. This terminal lug will be held down with a #4 bolt and ideally a locking nut. It wont come loose over time and will provide a very good connection to the chassis.
Now for this ground point I'd bring R4, C1, R6, R8, C7 and the ground connection of the Volume pot. These are all low current grounds and belong together. They are sensitive signals and should not be mixed with the power amp signals.
For the power amp I would do the same thing and install another terminal lug. The terminal lug must not use the PT bolts for mounting. To this ground pot I'd bring R9, C4, C5, C6 and the PT CT's for the HV winding and heater winding.
*If you really want to try to eliminate 60 Hz heater noise btw you can bring the heater CT to the output tube's cathode. Simple mod, no adverse effects on tone and easy to reverse.
There is a lot to say and read up on grounding in amplifiers but I'll just say
1. It's not good to use the chassis as a conductor for grounding
2. It's not good to mix low ground currents with high ground currents
3. Secure connections are key
Now the safety stuff
These are based standards and protocols set in North America not me. They are to be followed in consumer electronics to protect the user. So this isn't me being anal or anything
1. The PT mounting bolts should not be used as ground points or mounting points. Just because old Fenders did something does not mean it's right
2. The AC mains safety ground needs it's own dedicated ground close to the AC in point. Not on a PT bolt and not with the heater CT.
3. The primary live wiring should be fuse then switch not switch then fuse as the layout and schem show.
4. Wire nuts are a big no no. Heat shrinking and tying off is better. Ideally the unused wires could terminate on a terminal strip somewhere.
5. If it were me I'd add a 2W 220K bleeder resistor to drain residual charge from the filter caps when the amp is powered down. This is just personal preference through.