Some of your questions can't be answered real specifically until you pick a target. How much horsepower, how much torque, and where in the RPM range do you want to run? You need to have specific answers to these questions before, for example, you can pick a cam.
The compression ratio will depend on the cam you want to run. For example let's say you want maximum power in the 3000-5000 RPM range. A cam in the 235@.050" range for duration would get you there, and then a compression ratio of around 10:1 would be just about right for that. Pick the cam first, or pick several candidates, and post the specifications. Then decide yes or no on the stroker kit. With that information, someone here will be happy to run a DCR (Dynamic Compression Ratio) calculation on the combination with the different cams, and that will give you the optimum compression ratio. Milder cams need less compression, and more radical cams need more.
At elevated power levels, the stock rods are a question mark. With good bolts they will most likely live, but there is the off chance that one will blow up on you. Why chance it? Then, if you are going to buy pistons, rings, and rods, the step up to a stroker kit isn't that much, another $600 or $700 maybe. You asked how much the stock crank and rods will hold you back; without the stroker kit, you are leaving 50 ft-lbs of torque on the table. That would be a huge difference in a pickup.
Get that Streetmaster intake! That is an outstanding intake manifold for a 400-500 horsepower engine. It will be down a little on torque at low RPM levels compared to a good dual plane like an Edelbrock Performer RPM, but not much, and you won't even miss the torque if you go with the stroker kit.
On the heads, get what you can afford. The stock Edelbrock heads are excellent, and the Survival Motorsports and BBM heads are a step up from there. Good heads will help all across the RPM range, but for your combination I'd probably just go with the stock Edelbrock heads. They work well with the Streetmaster intake, and you can always pull them off and get them ported later.
The valvetrain options will depend on the cam again, and the spring requirements. You might be able to retain the stock rockershafts, but check them for cracks (see the Car Craft article). At least figure on getting the rocker shaft end stands from Precision Oil Pumps, because they provide support to the shafts that the factory rocker stands don't.
Last piece of advice - get the whole plan together before you buy anything. You want the whole package to work together, and if you change your mind about something halfway through the purchases, you may end up with a component mismatch that will cost you performance.