Nuts and bolts
One of the things I ordered early on was a timing belt and water pump kit. Given the engine had 80k miles on it, I figured it was just about due. Once I got around to removing the timing belt cover, I found a fairly new Gates timing belt was on the car. Given this, I ended up flipping the TB kit to a friend for a small loss (which I have recorded in my cost log).
But whats important is nuts and bolts. When I was removing the timing belt cover, I noticed that several of the bolts had pretty rusty heads. I ended up soaking them all over night in rust remover and they looked as good as new. The problem though was that about half of them had very poor zinc plating (a few seemed to have none at all on the head) and this was clearly what allowed them to rust. Re-installing them as is was just asking for a repeat of the rust build-up. Replacing them seemed costly at over $3 a bolt plus shipping for over a dozen of them. I considered having them powder coated when I send off the valve covers, but that seemed like overkill. I even briefly considered a zinc coating kit from Eastwood, but as i researched the kit I found myself reading about bolt treatments on a Harley forum. There I discovered the idea of painting them with fingernail polish. Durable, comes with a brush the right size for painting bolt heads, and easy to touch up if it gets scratched. A quick raiding of my daughter's nail polish collection and 30 minutes later, they were all painted black.
From there we go to Accessory bolts. One thing you will find is that most junkyards sell the accessories separate from the engine. I didn't even realize this until a few days after the engine was in the garage. I addressed this and sourced an Alternator and AC Compressor, but then I found I didn't have the bolts to attach them. I needed to order a weird gasket only sold by Honda anyway, so I ordered the 2 Alternator bolts and 4 compressor bolts. About 15 seconds after they were installed, I realized how much time and money in shipping charges my lack of thinking ahead was costing me, as now I needed to order a belt. Belt arrived and went on easy.