So technically you applied but got no response.
So any questions around applying needs to be answered yes but the questions around outcome in refusal you need to say no.
For the PCC it's better to get it for the last date you had surrendered your passport as technically it was the last time you had been the citizen of India.
As I said WES is for highest degree, so technically your highest degree is from Canada. Unless you are claiming points for Indian degree you don't need WES for that.
In that case keep an LOE ready in case you are asked so since you have submitted the application. But I don't think there would be an issue. Though just in case.
The sputum culture takes takes approx 8 weeks or so and xray is repeated after 3 months. Medical is an important part of immigration. One needs to clear medical to get through it so had to wait 3 months for xray.