For anyone working on engines, experience is often the best teacher. That’s true when it comes to the small things that you really never think about until Murphy’s Law takes a bite out of your backside. Early in my career, I was bolting an intake manifold on a small-block Chevy and discovered a few intake manifold bolts were missing. I hunted through my one-gallon paint can full of old bolts until I came up with what I thought would be a couple of suitable replacements.
On a small-block Chevy, only the four end bolts enter blind bolt holes. The rest of the intake manifold bolts are open into the lifter valley and four of these bolt holes line up or are very near a pushrod. If you use an excessively long intake manifold bolt, it can extend through the head and contact the pushrod. If the bolt is long enough, it will actually bend the pushrod by forcing it against the head. Not only that, but when the engine starts, the pushrod will still move, scraping metal shavings into the engine. None of these are good things.

You can see how this intake manifold bolt hole is nearly lined up with its nearby pushrod. A too-long intake manifold bolt will immediately bend the pushrod and ruin your day.
After I had torqued the intake manifold nice and tight and started the engine, it immediately began to misfire with some mechanical noises that indicated I had a problem. It took a while to determine that one of my substituted intake bolts was too long, and had managed to bend and all but mangle an intake pushrod. Lesson learned.
All of this can be avoided by using correct length bolts for the intake manifold. So it’s worth the effort to ensure the intake bolts are long enough to provide sufficient thread engagement but not so long that they extend through the bottom of the cylinder head and into the pushrod cavities.
The standard for minimum thread engagement is to have at least the diameter of the bolt worth of engagement. So for a coarse thread 3/8-inch diameter bolt with 16 threads per inch, this would mean a minimum of 6 threads worth of engagement into the female threads in the cylinder head.