Can taking high doses of vitamin d3, 5000 iu's daily for two years straight cause me to have multiple tiny kidney stones in both kidneys?

Maybe: This dose is well above what you'd need to prevent the deficiency in this vitamin that is so common nowadays, but is not outrageously high. Kidney stones are a hazard in extreme vitamin d oversupplementation but this dose is considered safe. You'd do well to take a look at all your risk factors -- genetic tendency to absorb calcium, fluid intake, composition of any stones you passed.

Calcium levels: Vitamin d per se does not cause stones; however, if taking a high dose of vitamin d may results in hypercalcemia, especially if you are also taking calcium, and high blood levels of calcium could lead to kidney stones.

Kidney stones: Vitamin d 3 as such does not cause kidney stones however, if you take calcium with your vitamin, as you are doing you can develop kidney stones.