You really need to find out what you have. The OEM bars run front to back, anything that runs across the roof is aftermarket so there should be instructions on line for fitting them.
When using a taper thread tap, you must take care to get it correctly threaded. The entire purpose is to cut metal so if you get it cross-threaded, IT WILL cut out the threads leaving you with nothing to screw a bolt into.
My technique is to get it started with fingers only, wiggle it gently until you feel it find the threads. Now screw it in by hand, only using the habdle when it starts to cut. Use plenty of WD40 or penetrating oil to help it cut. In your case it's cleaning the threads so should never be stiff to turn. You "can" use an ordinary spanner, but pulling on one side risks binding the threads. A proper die holder is well worthwhile for a job with no second chances.
When done protect the cleaned threads with copper paste.