Hey! you're in the same boat as I am, except I have a donor engine to run my car on while I rebuild it.
first things first, pull out your oil dipstick, see if it looks sparkly, if it does, rebuild your engine. If it doesn't, drop your oil pan. In the bottom of my oil pan there were literally inch and a half long metal shavings (make sure you empty all the oil out of the bottom it can hide it, best way is to run it through a strainer, in fact you can just do an oil change but leak the oil out through a strainer, before you actually pull the pan)
Basically metal shavings/dust = rebuild. Clean oil (well not clean but no metal in it) = the knock might be an easy fix that doesn't involve pulling your engine.
If you do end up pulling the engine and are looking for power adders, look into cylinder heads and camshafts first. There are tons of options out there for our cars, do a search.
Heads- you're already PI (performance improved, 99-04) and so what you can do is port your current heads (send them to the machine shop so they can make them flow even better), or you can look at something like trick-flow heads. Some members here make major power running through trick-flow heads, but personally I have no experience with them. (not 100 percent sure I'm even saying that right tbh).
Cams- don't get comp cams. They're cookie cutter generic cams, and for me personally it makes no sense to use a cam that is "universal" because being universal means power is left on the table. For the same price you could get your own cams custom ground, then you'd make more power AND you can have them set up for whatever you wanna do. Or you could look into buying totally new (not getting your current cams machined) aftermarket cams.
Personally what I am going to do is invest in a rebuild kit that comes with forged internals. This way I'll have a 0 mileage motor that can handle whatever power I wanna throw at it in the future, and I'll never have to pull the engine again (not to say I won't, I just won't need to). Then if i get rich enough for forced induction I'll be ready to go (tranny is also being rebuilt). Technically heads can be pulled with the engine in the car if you ever want to ugrade heads or cams, it's just harder, but it isn't like internals where you NEED to pull the engine to replace. Because of this I will spend MY money on internals not on cams/heads until later in life. (albeit it did not take me long to pull my engine and so I may go the route of pulling it again anyways if I wanted to do head work, but I wouldn't HAVE to.)
More power through internals/heads? raise your compression ratio! If you never plan on going forced induction (you'd want low compression in this case) go for a high compression build. I don't know enough to offer any suggestions on this, just remember higher compression=more power along with a tune capable of keeping your engine safe. Just remember though, you'll never get super high HP (350+ rwhp) out of a naturally aspirated 2v 4.6. (don't nitpick the NEVER, I just meant it wouldn't be economical) But if you do want to stay 300-350 compression is the way to go.
For me, until I have coilovers and insane suspension I'm not going to try and go for big power (anything over 300). Suspension work will get me not only faster than more power, but it'll handle better to. There was a member on here that had stock horsepower on a 2V 4.6 and was running mid 12's I believe with drag slicks suspension work subframe connectors gears etc and a good driver. Hard acceleration is fun, but wasting power by spinning tires isn't, and besides corners are more fun. (I autocross
)
If you want, I could upload a video of what my car sounded like and when I get around to pulling the engine apart I'll let you know exactly what was wrong in case you have the same issue I did.
first things first, pull out your oil dipstick, see if it looks sparkly, if it does, rebuild your engine. If it doesn't, drop your oil pan. In the bottom of my oil pan there were literally inch and a half long metal shavings (make sure you empty all the oil out of the bottom it can hide it, best way is to run it through a strainer, in fact you can just do an oil change but leak the oil out through a strainer, before you actually pull the pan)
Basically metal shavings/dust = rebuild. Clean oil (well not clean but no metal in it) = the knock might be an easy fix that doesn't involve pulling your engine.
If you do end up pulling the engine and are looking for power adders, look into cylinder heads and camshafts first. There are tons of options out there for our cars, do a search.
Heads- you're already PI (performance improved, 99-04) and so what you can do is port your current heads (send them to the machine shop so they can make them flow even better), or you can look at something like trick-flow heads. Some members here make major power running through trick-flow heads, but personally I have no experience with them. (not 100 percent sure I'm even saying that right tbh).
Cams- don't get comp cams. They're cookie cutter generic cams, and for me personally it makes no sense to use a cam that is "universal" because being universal means power is left on the table. For the same price you could get your own cams custom ground, then you'd make more power AND you can have them set up for whatever you wanna do. Or you could look into buying totally new (not getting your current cams machined) aftermarket cams.
Personally what I am going to do is invest in a rebuild kit that comes with forged internals. This way I'll have a 0 mileage motor that can handle whatever power I wanna throw at it in the future, and I'll never have to pull the engine again (not to say I won't, I just won't need to). Then if i get rich enough for forced induction I'll be ready to go (tranny is also being rebuilt). Technically heads can be pulled with the engine in the car if you ever want to ugrade heads or cams, it's just harder, but it isn't like internals where you NEED to pull the engine to replace. Because of this I will spend MY money on internals not on cams/heads until later in life. (albeit it did not take me long to pull my engine and so I may go the route of pulling it again anyways if I wanted to do head work, but I wouldn't HAVE to.)
More power through internals/heads? raise your compression ratio! If you never plan on going forced induction (you'd want low compression in this case) go for a high compression build. I don't know enough to offer any suggestions on this, just remember higher compression=more power along with a tune capable of keeping your engine safe. Just remember though, you'll never get super high HP (350+ rwhp) out of a naturally aspirated 2v 4.6. (don't nitpick the NEVER, I just meant it wouldn't be economical) But if you do want to stay 300-350 compression is the way to go.
For me, until I have coilovers and insane suspension I'm not going to try and go for big power (anything over 300). Suspension work will get me not only faster than more power, but it'll handle better to. There was a member on here that had stock horsepower on a 2V 4.6 and was running mid 12's I believe with drag slicks suspension work subframe connectors gears etc and a good driver. Hard acceleration is fun, but wasting power by spinning tires isn't, and besides corners are more fun. (I autocross
If you want, I could upload a video of what my car sounded like and when I get around to pulling the engine apart I'll let you know exactly what was wrong in case you have the same issue I did.