There's almost nothing height-specific in a pair of biking shorts.
335 km in two days is a lot of riding - 167 km a day is huge! You're going to be sore after that kind of ride no matter what.
Can you tell us more about the injury? I'll guess for now based on my experiences.
If your problem is in the bum muscles, then its a weight and saddle issue. No amount of padding will help if your saddle is too thin or too thick. Search this site for "sit bone width"
If the saddle checks out, it might be time for a bike fit. They're not cheap but they do pay for themselves in comfort. Us lanky types need extra consideration about how the bike fits, and how we fit the bike. You might benefit from putting a tiny bit more weight on your hands and on your pedals. Periodically get out of the saddle for a short sprint too, this allows the blood to flow back into the deprived areas.
A short rest every hour is always a good idea. Eat, 3-5 minutes of standing and you're good. Even standing over the bike is fine, as long as your posterior is getting a break.
I found that the more I biked, the looser my pants got because of weight loss over time, and as the pants aged the elasticity decreased. Together these add up to baggy pants, which induces chaffing.
reduce chaffing by applying petroleum jelly (or some specific+costly bum butter) to the areas before your ride.
If your pants aren't tight, they're too loose, so either take them in or buy new ones.
No gruds/undies/briefs/jocks/boxers/etc under biking pants/shorts with padding. Seriously.
I bought normal length pants because the waist was right, and they finish about half-way up my shins. This is not too bad because the ankles are exposed and provide a bit of cooling. And a place to sunburn as I discovered on one particularly sunny ride.
EDIT I just did a 12 hour bike ride yesterday, and my pants were fine. The Petroleum Jelly did well, so no chaffing the whole way. My only problem came from sunburned ankles, because I forgot to put sunblock on down there and as I rode, the pant cuffs rode up and socks rode down exposing skin.