1) how many miles on the car?
2) auto or 5sp?
3) what mods have been done mechanically? Don't care about a CAI or a drop-in K&N filter - just what has been done that could be a source of the noise? Clutch/flywheel? Maybe a bolt has backed out and is smacking something - and it is continuing to back out, which would account for the increase in noise. Cams? Maybe they weren't aligned properly when they got installed. Repaired timing chain guides? If so, did they take the chains off when they did them? If so, they could have misaligned stuff when they put them back on. Upgraded pistons? Could be valves smacking your pistons.
4) is your idle smooth and when you give it gas do the revs go up smoothly (sitting still, not driving)? When you drive it does it accelerate smoothly or is it jumpy/jerky? If it's all smooth, you can discount misfiring due to the coilpack. If it's jerky and NOT smooth, do #5:
5) get a spray bottle and fill it with water, then MIST the coilpack at night. if you see arcing, you need to do the coilpack fix.
6) after you do #5 (and fix it, if need be), is the knocking still there? Because I'm pretty sure it will be. If so, determine the LOCATION from which the knocking is originating - bottom/top/front/back/left/right - WHERE on the engine. Use a stethoscope if you have one. If you don't, get your longest screwdriver and put the metal part on the engine and your ear against the handle. Figure out where the noise is coming from.
I hate to say it, but I'd lean more toward incorrect cam alignment/timing chain slip. These 12v VRs are notorious for the timing chain guides going out on them. Not so much the chain, but the guides. And if enough of the guide went, the chain could have a lot of play in it. Enough for it to slip a tooth or two. I'd do what MkIV_03GLI said before you do anything else. The damage is already done - whatever it is - but hopefully not to the point you'll need an entire engine.
One other thing you might try, since you said you picked the car up and drove it about 50 miles so far. Interestingly enough, motor honey will hide a TON of noises. For about 50 miles. Go get some and pour it in - see if the car sounds like it did when you picked it up. I'm assuming either you just bought it or you're a mechanic. Either way, if motor honey makes it quiet again, rebuild it.
so the list of things to check:
location of noise
etc etc etc etc
hope you figure this out man...