Both sets of sentences are correct, the difference between them is the meaning.

Now this difference is a little hard to explain, but I will do my best.

The verb 'to have' conjugates in the present as 'have' or 'has':

• I, you, we, they, you all = Have
• he, she, it = Has

In the past, it conjugates as 'had' for everyone.

Now when it comes to questions starting with 'to have', asking if someone has done something, they are asking about one of two situations, each with it's own meaning.

When you use 'had' (past tense), then you are asking about any time up to a specific moment in the past.

Had you run a marathon?

Meaning "At any time up until that moment in the past, did you run a marathon?", or "Did you run a marathon by then?"

When you use 'have' or 'have', you're asking about any moment up until right now.

Have you run a marathon?

Meaning "At any time up until now, did you run a marathon?", or "Did you run a marathon by now?"

The difference between the two is the limit of the time asked about. When you ask using the past tense of 'to have', then the limit is referring to a specific moment in the past. When you ask using the present tense of 'to have', then the limit is this very moment, now.

• Have, has = "up until now"
• Had = "up until then"

I hope that helps!

Sure

As @TRomano already linked before denying his own research, plenty of people use the expression 'perform control(s)'.

Neither of you is wrong that the expression seems odd. The most common sense of control as a noun is the interface used to direct the actions of some device. The original sense was as a synonym for restraint or for a means of restraint. Perform doesn't work for any of those: apply is what happens to restraint and use is more common than either of them.

That said, the phrase in question shows up at ngram because other definitions of control exist. Its scientific sense as an experiment performed without a certain variable or factor is imminently performable. Its general sense as direction, management, or administration and its senses as a clipped form of control group, animal, &c. both suggest roles which can be performed.

More importantly, the original quote is not about 'controls' generally but about 'in-process controls' (IPC). That bit of jargon is defined as "checks that are carried out before the manufacturing process is completed". These are not applied restraints but inspections and procedures which should be performed during the manufacturing process to ensure quality control.

The discussion of 'control' and its definitions, apart from being largely mistaken, is aside the point. IPCs are procedures which must be performed and there's nothing ungrammatical about it.