You are okay of the marks line up, not To worry

Same thing happened to me, so annoying having to back-track. Anyhow, turned out to be a bit of the old gasket material on the block. Emery cloth sounds like a good idea...on the second attempt I used Permatex water pump & thermostat housing silicone rtv on the new gasket (thin coat) and under si...

it would not prevent leak from a major misalignment, and if ever replaced again (doubtful since each pump is good for two belt changes) its hard to clean up the rtv in the close space.

RTV for coolant, it's a special one. Put just enough so it doesn't leak inside when positioning the pump. Smear a little on both sides of the gasket. Hope that is an Aisin pump right ? About the only safe brand (or genuine) A razor blade to remove big chunks of old gasket, then a Stainless Steel Wir...

Just clean the surface up well and make sure it is flat. The gasket will take care of most "normal" imperfections. I have never used RTV when it wasn't required. Many do it for good measure - that is your call. Just make sure the "squish" does not get into the coolant system.

As Herman noted RTV isn't needed for the water pump gasket. When I installed the water pump earlier this year I just put a tab of silicone grease on the gasket to hold it in place. I scrubbed off the OEM gasket using brake cleaner on emery cloth. As mentioned cleaning up the RTV will be a hassle.