To answer your questions on valve springs no, do not run stock springs. Comp 911s or something similar. Take off springs from Stealth or Eddy heads would work fine too.

For break in what kind of distributor are you running? If its points get it pointed to number 1 and turn it until the points just start to open. If electronic get it pointing to number 1 and advance it a little, 10 degrees or so. Then snug it leaving it loose enough to turn if you need to. Plug in the vacuum advance.

Use a real break in oil, 30W is good. I used the Comp Cams break in oil. Dump it after break in. If you want to take a ride around the block before dumping it you won't hurt anything, but the sooner the better. After you dump it refill with oil with another bottle of break in additive. I would do this for the first 2 oil changes. 500 miles on the second batch of oil after break in, and you can increase the second oil change if you want. I change my oil often, cleaner oil is better.

Once you're done with break in VR1 or Brad Penn, either is fine. I used VR1 for my first few oil changes with a bottle of the comp cams additive. I put the Brad Penn in last time with the additive. Both of these oils have enough zinc and in a 20W50 both of these oils are extremely sticky and will keep your cam lubed when your engine sits so it wont be starting dry. I'm probably overdoing it adding the break in bottle to either, but I've got a 9 quart pan and rather be safe than sorry (too much zinc is not really good though, over 2000 PPM).

No truth to manifolds vs headers IMO, maybe they think the back pressure will help seat the rings? I say old wives tale. If its because of glowing headers they aren't running enough timing, which brings me to:

Pre-fill your carb bowls. If its a Holley remove the sight plugs. Pour some fuel in a dry water bottle and get a clean cap from a gear lube bottle. Trim it so it fits in the vent tube. Now fill the bowls until the fuel is at the sight plug bottom, just like setting the floats. Put the sight plugs back in.

Hook up your choke if you have it. Turn the curb idle screw in far.

If you've got the timing close it will fire up immediately. HAVE A HELPER. Hold the RPM above 2000 if the curb idle screw isn't enough. Have your helper adjust it until it is. If that isn't enough adjust the throttle cable to hold it.

Now check your timing. This depends on how your dizzy is curved, but shoot for 40-45 degrees with the vacuum advance for now while running at 2000-2500 RPM. This is conservative but should be enough to keep your headers from glowing/EGTs being high. When you're done you can get it dialed up perfect. Come back for tuning advice if you need it.

You can run water, no problem. Just make sure the engine will be out of close to freezing temps before you dump it. No thermostat? Might ask for trouble but should be fine. I'd put a 180 stat in it. If you run hot you have cooling or tune issues. If you can run half 110 leaded and half 93 pump for a break in on a street engine. The lead helps the engine run cooler.

Vary the timing. 2000 minimum, so have it set to run there or slightly over. Get behind the wheel and bring it up to 2500 and hold it every few minutes. I like to wack it up to 3K or so a few times in between it running at 2000 and holding it at 2500.

Once done get your timing set right. Then dump the oil and refill. With that cam shoot for a baseline of 15 initial, 34 total mechanical all in by 2500 or so, then find what the engine really prefers. I would run vacuum advance as well. Then take it out and put it under a load. Mat the pedal in high gear a few times, bringing the revs up higher each time (try to avoid a kickdown though, IDK if you have a MVB). Start 2K to 3K, back off. Let the engine slow down don't hit the brakes. Then 2K to 4K, etc.

Then go burn some rubber