I'm a little confused by your statement
"I have a 97, but I am doing just the heads swap, since I am building up the bottom end." From what I gather you are building up another bottom end on the side and doing the head swap on your stocker now? If so, I would wait and do it all together as a unit but I will post this info anyway.
I like to make it easy and remove the hood and cowl so you can get to the back side of the motor. The bolts that go through the timing cover for the new heads are thicker then the stock ones (10mm VS 8mm). On the 94-5's I had to make the holes larger on the cover to accept the thicker bolts. When you get the cover off test the new bolts to see if they "fit" and post your results. Are
you doing the building of the bottem end? I would strongly suggest having a experenced mod builder do the work on the block.
The EGR tube fitting is large so you will need a large wrench that can fit in a small spot if that makes any sense (you will inderstand soon enough). It can be a joy to loosen that beeotch on the exhaust manifold so you might want to let it soak overnite with some pentrating oil if you have the means. It will be eaiser if you loosen the fitting on the EGR valve first to give you some slack down below. The exhaust will have to be droped to do this BTW.
The power steering pump bolts can also be fun and I have found it eaiser if you remove the "clip" that makes sure the high pressure hose is secure(8mm bolt)
The 10mm bolt located under the line is the one that will piss you off. Use a small box end wrench and turn a little at a time. Be careful not to stress the High Pressure filtting when you remove the pump off the motor and tie it up on the body. This is a good time to drain the fluid out of the PS bottle. I would get a 1/4 inch swivel socket set or just get a 8mm swivel socket with a long 1/4 inch extension for the valve cover bolts. The middle passenger side bolts can be troublesome but the swivel socket will help you out here.
Once you get the timing cover off be sure to cover the exposed space in the oil pan so nothing can fall in. Align the crankshaft 10 degrees before TDC so when the chains are loosened the valves don't mash the pistons. You can use a vice grip and a rag on the non-lobe part of the cam to hold it from springing violently when you remove the tension off the chains. After the chains are off it's time to remove the heads. I like to use a impact socket and a breaker bar to loosen the TTY head bolts. Use rubber bands to "hold up" the bolts that hit the shock towers when trying to remove them so you can lift the heads off the block. Be sure to remember what bolts did not want to come out so you can preload them in the new heads and hold them up with rubber bands as before. Install the manifolds on the heads before they go on and route the new dipstick tube in the manifold/header drivers side head before you lower the head on the block. If you plan on installing new chains and the newer/stronger one piece crank sprocket be sure to also get the new thinner pulse wheel or you can have PIP dropout issues at high RPM's.
Be sure to torque all bolts and follow the steps for the timing marks as well as all torque sequences to the tee.
I would guess your noise issue would be a crank bolt coming loose if it was not torqued down properly. When you get enough stuff off remove the plugs and trun the crank clockwise and listen for your noise.
I'm tired and I hope you guys apreciate this long post that made my head hurt!
-Scott