First, let's clarify the timing "dots" on the cam/crank gear. Prior to 1967, the "dots" were shown to be positioned with the cam gear at 6 o'clock and the crank gear at 12 o'clock - or facing each other.
If I am correct, beginning in 1967 with the 400CI, the timing alignment went to 12 o'clock on the cam gear and 12 o'clock on the crank gear.
Why? I don't know. I see in my '68 Service manual a photo of the rotor in the "No. 1 position" which is actually the No.6 position. HOWEVER, I can see some of the carb in the photo and it is a Rochester 4-Bbl which indicates an older engine, pre-1967. Manuals are sometimes not 100% accurate and do slip in some "older" photos. So the reason for th "dot" alignment change is most likely due to a re-design in the distributor - possibly the position of the vacuum advance and its relationship to the engine and its movement for adjustment?
However, either position will work, so no need to rip apart the timing cover and pull gears & chain. With the timing dots are aligned at 12 o'clock, the number 1 piston is put at the TDC firing position. When the dots are aligned with cam gear dot at 6 o'clock and crank gear at 12 o'clock, the number 6 piston is put at the TDC firing position - making the No. 6 the new No. 1 and then you follow your firing order from there (timing is 180 degrees off).
Of note, and mentioned this before, I used the dot-to-dot alignment on a '68 GTO gear/chain replacement thinking, and being told, that this was how you did it, right? Wrong. The engine would pop & sputter and sometimes almost run depending on where I moved the distributor. But, it would not start. So I parted out & junked a perfectly good running car (a $250 purchase back then) because I thought the engine bit the dust when the chain broke on me. If I had only known. :banghead: So that should clarify the timing gear "dot" alignment.
Seeing your engine is running, but timing off a bunch, my experience says it would not run at all, let alone pretty good, if the timing dots were 180 degrees off from the get go.
Make sure you are using the No.1 plug wire for timing and keep other wires away. I clamp my clamp down by the spark plug and away from other wires, not up top at the distributor cap.
To do the timing tape thing, I feel it wouldn't be as accurate as it could be with the best way to do this is right when you align your timing gears and use a timing wheel and piston stop with the heads off. This I would think to be the most accurate way to find TDC and then affix the timing tape as lined up with TDC on your timing cover indicator "0". Now i have never applied, nor used a timing tape, so my thinking on this may be wrong. I also have a timing wheel and piston stop and have never used them, but they look impressive in my Craftsmen tool box draw. LOL
You can certainly still get close using a piston stop that inserts into the spark plug hole and knowing both intake & exhaust valves are closed as the piston comes up on the compression stroke. This could be used to see if the timing gears were not aligned straight up as your timing mark on the balancer will be off. Here is one type of a piston stop:
https://www.summitracing.com/parts/...MIypCv98SB5QIVjobACh1owgx7EAQYASABEgJusPD_BwE
There was a forum member (and I simply could not find the post as it may have been a spin-off of another post we had going) where his timing was also way off as yours. Turned out it was the crank gear. It had multiple keyway's so as to advance or retard the cam - many crank gears use this adjustability. He had misread the gear as it was poorly stamped and aligned a keyway marking when indeed the alignment dot was slightly to the left, and not having a keyway slot below it. He had even posted pictures and that was what I was looking for as you could see how lightly the correct alignment dot was stamped. Once he corrected that and put it all back together, the timing was perfect.
So this could be the issue if you used a crank gear having several keyway slots to advance or retard the timing of the cam through the crank gear. The piston stop as mentioned earlier might be an indicator of this before you go pulling things apart.
Found another "weird" fix on the H.A.M.B. website. A member was having the same experience. All kinds of suggestions, none of which worked. The fix? The distributor cap. It seems he installed an exact same second distributor to see if it was a defective distributor. Same results. Then for some reason he decided to try different parts on the distributor, part-by-part. First was the distributor cap swap with a different one he had. Bingo, timing went to where it should have been. So the cap (maybe made in China) was somehow causing an effect on the timing reading at the crank. I can't imagine how, but who knows. Very "weird" and I have never heard of such a thing, but......... So as simple as this sounds, maybe go to your favorite auto parts store and get another cap. If it works, great, if not, then you have a spare all ready to go when you change out the cap when it wears out. I like a distributor cap with the brass contacts over the aluminum. This is what I always try to get if available.
If me, I would not invest a lot of time in this as long as the engine ran good, no overheating/pinging, and you can time it by ear/feel. My last 400 build I could not get it to time using the timing mark on the balancer & timing cover no matter what I did. So I gave up and just timed by ear/seat of the pants. I am constantly learning things myself and when I tore the engine back down to inspect the damages (lost oil pressure), I learned at that time that I had a crank hub, not a harmonic balancer. The hub was used on later production 1970's low performance 400's. It was solid and very small in diameter, so it would not work on the 1972 timing gear cover's scale. It was a junkyard engine and bought that way be me and reassembled that way by me. Who knew? It ran fine, but always had a slight vibration, now I think I know why. :yesnod:
So it is up to you on how you want to proceed. You can continue checking your timing, timing advance - looking for worn/loose parts, stuck weights, weak/missing springs on the weights, new cap/rotor, or pull the timing cover and check the timing gears and dot alignment again. You could use a piston stop and see how close your timing marks actually are in alignment to verify the mark on the harmonic balancer is correct.
So whatever you try, keep us posted of the results and we should be able to narrow it down and get things right. :thumbsup: