1) Where does the current flow to?
Through the resistor then through the opamp output to the negative voltage rail (not to the ground at the positive input, in normal circumstances essentially no current goes into the inputs of the opamp ... it's essential to operation of the TIA). The opamp generates whatever negative voltage at the output which is required to make the bottom of the load and the negative input be at ground potential. The opamp does need to be able to sink 200 mA, which rules out most precision opamps without some kind of booster stage.
2) Is that how you would more or less connect the different stages or is the image you provided in place of the OP1177 ?
You need the circuit from 3a, the output from the TIA will be a negative voltage and only the 3a circuit will convert that to a positive differential signal for the ADC (I think at least, this isn't quite the way they mean it to be used ... it's meant to work with a positive voltage, but I think it still works with a negative one).
3) Is this only capable of low side sensing ( doesn't matter just asking)
This specific configuration yes, but the concept can also work high side.
Iv attached another picture, of a possible setup, not sure if this is what you mean? So the burden voltage will be sinked through the 1R that will produce 25uA at 1uA Load and 5mA and 200mA load?
You still don't get what a TIA does, what I called the sense resistor is actually usually called a feedback resistor. Probably better to call it that.
That 25 Ohm resistor you drew in shouldn't exist. The feedback resistor needs to be 25 Ohm. The bottom of the load is directly connected to the negative input of the opamp ... just like I drew it.