This is the unit that is currently installed and working but i believe it's not wired properly.
Serial Number: 18011060886
Model Number: PA250AC
Power Code: 01
Control Code: 11

Picture imediatly below shows how the furnace is currently wired. (how it was wired when we bought it used)

Picture imediatly below shows a wiring diagram similar to the wiring and components of our furnace, but not exact.
This is a picture from page 32 of the wiring diagrams pdf for models PA and BA gas fired unit heaters. For full manual click here.

Here is a blank copy to draw the connections how they should be made if necessary.

Question: What does the H, T and C mean on the transformer? C for Common, T for Thermostat and H for Hot (as in power/line/feed wire)?
Answer: _______________________________________________________________________________________

Question: How does electricity flow through the circuit, can you walk me through it please (essentially how does the wired circuit components function/as electricity flows through the circuit.)
Answer: _______________________________________________________________________________________

Question: I hooked up the Main valve TH (Thermostat) to the transformer because it looked like a wire was missing. Was this correct? I’m thinking now I should have hooked that to the thermostat and the other wire of the thermostat to the T or the H terminal on the Transformer would you agree?
Answer: _______________________________________________________________________________________

Question: How does the 3 prong limit control work in this unit exactly? My other Modine heater units only have a 2 prong/terminal limit control (red and blue wire only). Could you explain how those work in comparison to the 3 prong one please?
Answer: _______________________________________________________________________________________

Question: Are the Transformers output AC or do they convert to DC? I think it stays AC correct?
Answer: _______________________________________________________________________________________

Question: Are the H & T terminals on the transformer essentially the same thing (redundant) so that wires could be ran from either/or (interchangeably). (So whether or not they are jumpered [which they are] it is irrelevant correct? If so why then would there be more than just 2 terminals? I checked the voltage at both H and T off of C and they were both about 25 to 27 volts so I would assume they are interchangeable/redundant.
Answer: _______________________________________________________________________________________

Question: I cut the blue wire in half and spliced in series the thermostat. It works and the valve opens and the burners ignite when the heat drops below the number set but was that the correct way to wire it or is there a better way. Also the fan would never kick off with this configuration so I did the same to the red wire running between the fan timer and the limit control to power up the fan part of the circuit at the same time that the main valve gets power (via the switching in thermostat due to room temperature.) It works and the fan comes on about 20 seconds after the burners are lit and running and furthermore shuts off when the main burners shut off but was that the correct way to wire it or is there a better way? I found out that is bad because the red wire back feeds through the blue one and the fan comes on right away (maybe if I used different wires altogether to run to the thermostat than sharing the same wire that I used to do an in series splice in the blue wire to the thermometer.
Answer: _______________________________________________________________________________________

Question: Is this a good scenario… Wire in the thermostat just after the Disconnect Switch before power connects into the junction box of the heater unit so that the thermostat is the “gate keeper” controlling whether or not the circuit gets power or not depending on the temperature set. Probably would need like a high to low voltage relay or something so the thermostat wouldn’t  get fried by the high voltage correct?
Answer: _______________________________________________________________________________________