I'd contact Stephen directly...it definitely looks like you got a different spec transformer.
Check for continuity between the two black wires. Based on the color scheme of the other wires (red, green, yellow, striped), the 2 black wires are most certainly the PT primary wires (hopefully for 120VAC). If this is the case, you would do the following (assuming you haven't done any other wiring than what you have in your picture and your heaters are all wired in down to V1 and there are no "loose ends". The star ground should be firmly tightened and the green/yellow and red/yellow soldered to the tab):
Run a wire from the Line of the IEC socket to the end of the fuse holder. Run a wire from the side of the fuse holder to one side of the power switch. Connect ONE of your PT black wires to the other side of the power switch. Connect the remaining black wire on your PT to Neutral of your IEC socket. This will now complete the fused, switch circuit from the IEC through the PT. Be sure to firmly connect the IEC ground to the chassis as described in the manual.
Install a fuse into the fuse holder. Ideally this would be a smaller value than you would normally use (e.g. 0.5A) but you can use the 2A that normally would go in there. Without any tubes, and making sure your heaters are all connected (also check for stray wires underneath the indicator lamp so you don't short out to the chassis), turn on the amp just to make sure your indicator light comes on. If it does you can go to the next step.
With your meter set to VAC at a setting that allows for reading up to 400VAC (if your multimeter is not autosensing), connect your ground probe to the chassis (follow safety procedures in manual). With the amp turned on and one hand behind your back, check the following voltages and write them down:
IEC socket, Line (should be ~120VAC)
Pin 4 of rectifier socket (should be ~350VAC, probably 10-15% higher since the transformer is unloaded)
Pin 6 of rectifier (same as pin 4)
Each side of the heater supply should read 3.15VAC to ground, probably a little higher since you aren't drawing current.)
Now touch the black probe to pin 2 of the rectifier and the red probe to pin 8. You should get 5VAC (again, maybe a little higher).
Turn off the amp.
The above procedure is taken from here:
https://paulrubyamps.com/info.html(The website seems to be down at the moment, but I've recently accessed it so hopefully you can get to it).