I haven't encountered green gunk in a brake system. It might result from a wheel cylinder sleeved with brass. Old, decayed brake fluid with high moisture might attack brass and generate a green oxide.

Concerning the persistent clunk on takeoff:

One thing to check is the drive shaft slip joint, which is allows the driveshaft to telescope slightly when the car goes over bumps and when taking off from a stop. The splined shaft and sleeve need to be clean and well lubricated. Sometimes old grease can accumulate and prevent the parts from moving freely and having full travel, and an assembly that is not well-lubricated may bind under torque load and then release suddenly, making a clunk or bumping sound. It's also important that the slip joint be assembled correctly so that the u-joints will be "in phase". The Packard drive shaft has arrows on the slip joint extenion on the driveshaft and on the yoke to show when they are in correct alignment. Incorrect alignment can cause driveline vibration and rougher clutch engagement by causing the u-joints to fight each other each time the driveshaft revolves.

Mild occasional gear clash when shifting might be related to a dry transmission input shaft spline or a dry input shaft pilot bearing. (Or a worn synchronizer) Low mileage cars can have these conditions due to age, or in the case of prematurely worn synchronizers, a previous driver may have had the bad habit of not fully depressing the clutch pedal when shifting gears.

If you have had the head off the engine, did you carefully clean the block and head surfaces, paying special attention to areas where the head studs go into the block? All surfaces right up to the studs need to be clean and flat. Studs and stud holes in the head must be free of rust and scale. A new gasket should be used, and the head should be installed and the nuts tightened in the correct specified pattern. It's best to tighten them with a good torque wrench in 3 stages of about 1/3, then 2/3, then full recommended torque. Then, after filling the engine with water and running it for 15 or 20 minutes at light load or idle, it should be stopped and allowed to cool down, then the nuts retorqued to spec with the engine cool. At that point, I'd go for a short drive of a few miles at lower speeds and avoiding any hard pulls, then let it cool down again and again check all nuts for proper torque. Do any checking and tightening in the correct pattern and do not exceed recommended torque.

Most lifters will spin. Ones that don't may be gummy or worn. A valve not opening fully or with too little or too much clearance will also not be timed correctly. Too little clearance will cause the valve to open early and close late and may cause valve overheating and could even prevent the valve from fully seating.

Too much clearance will cause the valve to open late and close early with reduced total lift. These problems usually would not affect the engine to the point of having an outright miss, though a tight valve not seating fully might either by causing low compression or by causing the valve to stick.

A light miss under load or a "floating miss" can be hard to pin down, but is most often ignition related.

A screen and bowl type filter might work on the suction side, but it would need to be kept clean and absolutely air tight. You'd also need to keep it away from any source of heat to avoid "vapor lock" issues. A large filter would be preferred over a smaller one. Any restriction in the fuel line from the tank to the pump will cause trouble.

Valve noise that comes and goes often indicates gummed lifters.
A miss under load is often a problem in the ignition system. It could be a dirty, worn, mis-adjusted, or otherwise defective spark plug, a plug cable that has leaking insulation, a problem with the distributor cap or rotor, a coil issue, low primary voltage, or some problem with the points. Spark plug cables can look good and still leak high voltage to ground. Ignition system parts need to be clean, inside and out, that includes the distributor cap and rotor, the coil, all plug wires, and the spark plugs both the firing end of the plug and the insulator where the plug wire attaches. Spark plug wires that have rubber boots at the plugs can deteriorate and allow a spark to jump form the boot to the plug body which will cause a miss. The more load the engine is seeing, the more voltage is required to fire the spark plugs. That's why a miss that shows up under load is very often related to some problem in the ignition system.

Engines that have the plug wires inside a metal tube or holder of any kind often have plug wire shorts to ground within the metal tubes or shields.

Radio resistance/ radio suppression type spark plugs and spark plug cables do not work well on older ignition systems not designed for them.

"Vacuum is nice and steady, that is, needle does not flutter."

That's good news. That indicates that your valves are sealing and holding compression, at least at idle.

Valve noise is normally a clearance issue or a lifter issue, and may not affect valve sealing.

Valves can somtimes work well at low speeds, even if some noise is present, but fail work well at higher speeds due to sticking issues or weak springs or both.
Driving the car at moderate speeds for a few hundred miles can resolve sticking issues. Weak springs need replaced. Rust pitted springs need repalced. If an old engine has one or more weak springs, it's usually best to replace all of them.

If you are located well above sea level, vacuum and compression test readings will be a little lower than specs. At higher elevations, initial timing settings can be set earlier than spec.

Ignition point gap affects both timing and overall system performance. If your car has a dual point distributor, special procedures may be needed to set the points correctly.

Putting new lifters on a used cam may not be a good idea. Mixing the positions of used lifters on the cam may not be a good idea. If you continue to have issues, I suggest removing all of them, keeping them in order, and take them apart and clean and inspect them. Do not mix parts from one lifter to another, ever! Hydraulic lifters have a limited range of function, and need to operate within that range, which typically requires an initial adjustment. Factory procedures and specs would need to be followed. The lifter needs to be able to expand when the engine is cold to maintain proper valve clearance, and collapse slightly as the engine warms up to maintain proper valve clearance. A stuck, bottomed, or topped out lifter plunger cannot do this.

I'd want to run the engine several hundred miles at moderate speeds to allow the fresh oil and Marvel oil a chance to clean up the lifters, rings, etc. Any cleaning effect will occur when the engine is warmed up and running. I'd keep the engine speed down, with road speeds in the 45-50 MPH range or less. Longer runs are better than shorter runs. The idea is to get the engine warmed up and running, and the hot oil circulating. Runs lasting an hour or more are best. If you have an oil filter, I'd start with a clean element. Correct any missing or other tune up issues. You want the engine running on all cylinders.

I would get rid of the filter between the tank and the pump. Any filter should be located on the discharge side of the pump. Filters on the suction side of fuel pumps are notorious for causing trouble.

All hose clamps on rubber fuel lines are subject to loosening, especially on cars that have sat idle. I'd snug all of them up. If you have a way to empty your fuel tank, I suggest blowing compressed air into the tank (with the cap OFF) through the fuel outlet line.

Some tanks that have been cleaned and coated have a restricted fuel outlet line. This can cause fuel starvation, especially at highway speeds in hot weather.

I'd remove the fuel filter between the tank and the pump and NOT replace it. I'd also cut open and visually inspect the filter. If it has much debris in it, you probably need to remove and clean out the tank.