There have been many small...
There have been many small changes to the Gen III since it was introduced in '97. One example is the valve covers: The '97-'98 Gen IIIs had perimeter bolts, while the '99-and-later valve covers were center-bolt designs. This makes it easier to identify what year heads and valve covers you are looking at.
The LS1 Gen III V-8 nylon-intake manifold is impressive with its low height, minimal turns, and high-flow numbers. The early LS1 intakes should all be replaced with LS6 or LS2 intakes, as the improvements in manifold volume, throttle size, and port shaping make the LS1 intake a detriment to power output.
The truck intakes have a much different design; they certainly won't win any appearance contests. The main reason they look different is that the inlet needed to be 3 inches higher than the LS intakes in order to clear the cooling fan. The 4.8, 5.3, and 6.0L intakes are all common, so there is no gain from swapping one for another.
The LS2 intake (GM PN 89017648, available from GM Performance Parts) is a bargain, and many believe it flows just as much as the aftermarket intakes. Installing it will require some rewiring work as the manifold pressure sensor is moved from the back to the front, and the factory LS2 throttle body has a different bolt pattern than the LS1 unit. Also, the 90mm LS2 throttle body is electronically controlled, so either an aftermarket, mechanical throttle body will be required or an adapter for the existing throttle body.
The act of torquing down stretch-to-yield...
The act of torquing down stretch-to-yield fasteners (which are used on the head bolts, main cap bolts, harmonic balancer, and other major components) goes like this. First, the underside of the fastener head is lubricated, and the bolt is torqued to the minimal level; then using this torque angle socket (shown), a specific amount of additional twist is applied to the bolt. Often, the twist is added in two steps, like on the cylinder head bolts.
The LS1 Gen III V-8 architecture is sensitive to the components that support it. These include the inlet that provides air to it and the tubing that guides the exhaust out of it. The electronic controls [what GM calls the Powertrain Control Module (PCM)] and the calibration inside the PCM are also a big part of the power production of the Gen III V-8.
Since most of these components are built for 95 percent of the population, which doesn't care to hear the engine doing its thing or want that last 5 hp from the combination, there are power increase opportunities here.
Adding small amounts of power is easy with open-element airboxes and smooth-inlet tubes, after-cat exhaust systems, tube-exhaust headers, and calibration reprogrammers. All of these components are relatively straightforward to install, qualifying as "dry" components in the business since they don't require the installer to touch the oil, fuel, coolant, brake, air conditioning, or power steering systems (many of which require special tools, equipment, and knowledge to properly reassemble).
The LS1 Gen III V-8 responds to all of these modifications, but the most impact will come from installing long-tube headers. These headers are complex and expensive to install but point out the choke point on the vehicles. The exhausts are built to be low cost, durable, and emissions compliant, not to generate maximum flow, and the losses in flow do make a big difference in power output.
The long-tube systems usually require a completely new exhaust, with aftermarket catalytic converters and other components, so they are expensive, but if you've made other modifications and want to truly reap all the benefits of the changes, the stock manifolds will need to be swapped out at some point.