Like Ron said, You need to hold the throttle wide open when doing a compression test. Otherwise the cylinder will not fill with enough air to get an accurate test. You should have a battery charger on the battery so each cylinder is checked with a full charge on the battery. You should pull all the plugs so the engine can crank faster. That's officially how its done. I've done it without doing any of that stuff and have gotten good readings but since your readings are bad you probably should perform the test correctly.
If this was a quality rebuild, its unlikely all the cylinders have poor compression after only 2000 miles. I try a different compression gauge just to verify yours is accurate. You can have a faulty compression gauge and the problem could be elsewhere.
The first thing would be to give each cylinder a squirt oil and see if the compression comes up. The oil gives the rings a temporary seal. If the rings are bad the compression will come right up to specs with a squirt of oil. If you got the engine hot the rings could have lost their tension.
If one cylinder was low you would look for a valve problem, worm cam lobe, broken ring, blown head gasket on that one cylinder. But when all cylinders are low you look for something common to all of the cylinders. If it had a timing chain, it could be stretched. But with gears its unlikely it jumped a tooth. It would probably strip a tooth off and then not run at all. If you had timing marks on the crankshaft pulley you could check it to see if the timing had changed do to the gears not being aligned properly. Always make timing marks and a pointer on your flatheads when you have the heads off!
A plugged exhaust can be checked with a vacuum gauge. I've mostly seen it happen with melted catalytic converters. It happens a lot on those cars. But mufflers can have baffles break loose and then cover the outlet hole. Usually you will hear a rattling muffler. It acts like a governor and will only let you go a few mph but it doesn't run bad it just will only go so fast and it cause the engine to run hot. I suppose a rodent could build a nest inside the pipe or you could run over something and collapse the pipe. You could try separating the muffler from the inlet pipe and see if it makes any difference. You could also do a compression test with the muffler disconnected. I think thins is unlikely your problem, it's pretty rare, at least here in SoCal. Here is a video showing you home to check it with a vacuum gauge. They are neat tools, everybody working on cars should have one.
https://www.ericthecarguy.com/faq/s...g-a-vacuum-gauge-to-find-exhaust-restrictions
You can also take a rubber tipped air nozzle and with the piston at TDC blow air into the cylinder and see where it comes out. If it comes out the intake the intake valve is burned. Out the exhaust, the exhaust valve is burned. Out the radiator you have a crack or bad head gasket. Out the oil fill the rings are worn. Some air will normally get by the rings. The only way to accurately test them is with a special tool that measures the percentage of leakage. Without that tool about all you get check is for a major failure like a hole in a piston.
