You can't really test them with the Audio Probe, you trace the signal of your guitar along with the schematic and see where it stops as that's probably your problem. We'll just assume they're okay for now though.
With Rebiasing, you need to change the value of the resistor going to Q3s Collector (The 8k2 in this case) normally you'd do this on the breadboard beforehand and just solder the correct resistor value in according to the value of that or use a Trimmer to adjust the resistance untill it biased correctly, you just probe it with your multimeter untill it reads the correct reading.
You'll have to unsolder whatever resistor you having going there now unless by sheer luck it reads around 7 Volts already (it's rare but this can happen with stock resistor values)
You want to ground to the board yes and then send a wire from the ground to the jacks as they'll ground the pedal through the enclosure.
The Input ground is good practice, it helps stop oscillation in bypass among other things if a pedal has a tendancy to do that but for the sake of ease... it might be better to go with the second drawing, although heating and re-heating a switch too much will damage it. It'll only mess something up if you've done it wrong, if you followed the diagram you'll be okay...
Although, i've just noticed something... this pedal should be positive ground and the wiring diagram provided is negative ground... that's not going to help you one bit, you need to swap your battery connections and if you're using a DC Jack... you're gunna need a new power supply most likely.
I'm sorry to say but this was not a good choice of first project
next time... i'd suggest a simple boost kit with some comprehensive instructions, this is more for the intermediate builder for anyone that might be considering it.
(pretty sure this is required for one's first pedal)
