I've learned a thing or two about brakes from sports car racing, so here are my thoughts:
Rotors rarely warp. Pedal pulsing is usually caused by uneven transfer of friction material from pad to rotor. In race cars we deal with this by repeatedly hard braking from 120mph down to about 30 to get the rotors really hot and scrub off the friction material. Probably not an option for you. You can try polishing the rotors with some emery cloth if the pulsing bothers you, but it doesn't really affect braking performance.
Are you having problems like brake fade? If this is the problem, changing your braking technique and/or adding additional cooling ducts to the system can help. Is your rig over GVWR? If so, you're asking for trouble and you should look to reduce weight or get a bigger truck.
Not sure what you mean by a brake upgrade. Bigger rotors and calipers can help, but that's a huge investment, $1000+. If it's time for new pads, look for a heavy duty truck pad like Hawk LTS. Get new rotors - OEM are fine - and do a complete brake fluid flush.
If by stainless steel lines you mean the flex lines with braided stainless covering, those can add abrasion resistance and some people say they give a firmer pedal feel, but they don't increase stopping power.
Swapping the rear drums for disks probably won't do anything unless your rear brakes are locking up. If you put disk brakes on the rear you'd probably have to change the proportioning valve as well so you don't screw up the brake bias.
Tires are an often overlooked component in the braking system. Make sure you have the right tires for your truck, properly inflated and not worn out.