Here's what caught my eye... oil pressure. 40 at idle is fine, but take a look at the temp gauge too. my stock 6.5 will almost peg the oil pressure gauge at cold idle. Then near the end when he revs it, the oil pressure doesn't rise much at all.
Its possible you lunched a main or rod bearing, but it sounds more like a valve issue. Mains and rods tend to clunk more than tick. If the smoke is blue, its oil. If its white, its diesel. If its diesel, you're in for injectors most likely unless the timing is way off. If its oil, you're in for at least rings.
But, the good news is that the rest of the truck looks nice, the alternator looks brand new, and even if you have to rebuild you still have a really nice truck.
The stock 6.5 has a couple weak spots. First of all, move the injector computer away from the engine. It can't take the heat and likes to die. Many aftermarket companies sell kits to do this, or you can get creative. There is rumor that the block decks and/or head decks are thin on the civilian models, but I've run two of them senseless and never had a head or block failure, nor a head gasket failure. But if you want to remedy that issue, just get a military block to replace it.
Stock HP ratings were 180-200, but don't let that fool you. They make more than enough torque for towing. If you want to up the ante a bit, intake and exhaust FIRST. That should give you a nice boost, but if it isn't enough go with a mild chip and an EGT gauge. With diesels you always improve airflow first, then add fuel. If you do it the other way around, your EGTs will spike and damage the turbo. Keep EGTs 1200 or less and all will be well.
What I would do first is use the screwdriver-to-the-ear trick to narrow down where the noise is. If its up top, pull the valve covers and diagnose what's wrong and fix it. Have spare valve cover gaskets handy since most of them came with cork/rubber gaskets that will leak if you try to reuse them. Then check the injector timing to see if the smoke is from retarded injection. Maybe pull the injectors and have them tested and rebuilt if necessary to get rid of that smoke... unless that's oil smoke in which case you'll need a whole rebuild - the extent of which can be determined between you and your machinist.