The RPMs seemed to decrease just a bit, but it kept running.
That would be the effect you would find, the engine will slow but won't stop as the other three cylinders are still working. At a higher idle speed the engine would run a little rougher than when you aren't earthing out.
When you earth a cylinder and there is no change in rpm, then that is an indicator that is a 'crook' cylinder. Remove and clean plugs set gap to around 30thou and try again.
Remove coils check all contacts are clean and all wires firmly fixed (loose wires can be a big cause).
From your explanation it sounds to me like a timing issue, possibly fuel, but probably miss timed.
I am not familiar with your part of the country, but can you reach out to a local T club chapter of this club (or the MTFCI - the 'other' T club) as a visit from a long time T'er will quickly help pin down the issue (and will make new friends as well

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When changing up, I would do so at much lower speed than 13mph, that is a bit fast for the engine (low really is low). Back the throttle off and lift your foot smoothly and smartly (don't 'slip' it off). You shouldn't need to adjust the spark advance. When starting remember to retard the spark, then advance it again when running - rule of thumb is to advance as far as you can, (I know the diagram gives different positions for different driving conditions but actually, moving it to advance and leaving it there works just fine too. With experience you will find the 'sweet spot' for your engine (It seems each one is different), but I would not worry about finding it until you sort the other issues.
Juddering on the change up could be the clutch needs adjusting a little. There are a lot of 'could bes', most are 'easily' fixed, but figuring out which one is usually a bit of an issue, which is why we suggest looking for a local branch of either of the T clubs.
Cheers, don't be discouraged! it will be clear as you gain experience. And when it runs as it should that opens up a whole new time of enjoyment.