I take a multi-vitamin and drink a protein shake daily. My vitamin markers are way over. Is this ok?

As I understand it, yes. Your body uses what it needs and disposes of the rest. As a general rule, RDA values are set to avoid deficiency, but our bodies typically need more to function optimally. I take the 100% as a minimum value, not a maximum, when it comes to vitamin and minerals. Obviously this varies from mineral to mineral and person to person.

For example, US RDA for Vitamin D is 400 IU. That value was set decades ago to fend off Rickets. Many professionals now believe we need 10x or 20x that for our bodies to function optimally.

I'm not giving you medical advice on what you should do. I'm merely telling you what decisions I've made for myself.

There is also the question of absorption rates of the individual elements. You will find discussion of when to take a multi vitamin and even debate about the value versus aiming for specific supplements

It depends on how over you are the RDA thresholds and which vitamin. Some are water-soluble, some are stored in fat. Yes, you can have a toxic level of vitamins. https://www.mountsinai.org/health-library/poison/multiple-vitamin-overdose

You might not need the Centrum supplement. I think it's worth sharing your data with a registered nutritionist. Just have one or two consultations. Also keep in mind that if you take biotin for example, this could change your lab results for cardiac markers. I think vitamin K also for people on blood thinners.