That sucks. Those caps are the shims for your valve adjustment. You'll have to mix and match them until you get the right valve clearances.
When I rebuilt those types of engines, I would number and measure the thickness of all of the shims and make up a chart. Then I'd install them and measure the gaps. By figuring out where I needed thicker or thinner shims, I could swap them around to get the gaps into spec. Next time, try using and egg crate to hold all those little parts and keep them in order. I like using plastic baggies labeled with a sharpie marker, too.
