The Yellow Cheeks came first, then Red, then back to Yellow.
The first product available to the public was the Demo Booster.
You can see which Pikachu was inside the Demo Booster HERE at 2 minutes 38 seconds.
Shadowless cards had multiple print runs.
WotC was hoping that we wouldn’t be able to tell the different print runs apart.
Here’s an additional way to tell the Japanese cards apart from WotC cards.
carefully compare the card width & height.
WotC cards are 63 mm wide by 88 mm tall, which is a European standard playing card size, because the first print facility WotC used for Magic cards was in Belgium, and they stuck with that size for everything, even in the USA.
The Japanese made cards have slightly smaller dimensions.
See the picture below.
The yellow border card (face up) is WotC (Euro standard) size.
The smaller card (face down) is Japanese size.
The biggest card shown here isn’t relevant to this discussion, but it’s a special glossy card from WotC headquarters, and it’s USA standard size 2.5 inches by 3.5 inches.
As you mentioned, this card comes from a Shadowless theme deck, not from a 1st Edition booster pack.
That makes it a misprinted Shadowless card, not a misprinted 1st Edition card.
This misprint was available in December 1998, before anyone had 1st Edition booster packs.
That theory isn’t correct.
The best explanation for what happened, can be found HERE.
Let’s put a small section in chronological order. 
For WotC cards, Demo Boosters were the first product released to the public.
Demo Boosters contained Shadowless Yellow Cheeks.
You can see it opened here.
(Japanese CD Promo is based on this card, but I think WotC released other cards faster than Japan could print and distribute it)
In December 1998, we have Shadowless Yellow Cheeks with Ghost Stamp misprint, in the ZAP! Theme Deck.
You can see it opened here.
I’ve heard the Japanese CD Promo was released in January, but I’m not sure what day.
Maybe you can figure that out.
Next is 1st Edition Thick Stamp with small D Yellow Cheeks, inside the earliest 1st Edition Booster Packs.
There is a 2D stamp, and also a misprinted 3D stamp.
It sounds like most of them were misprinted.
Afterward, they fixed the Trap Settings problem that caused the 3D stamp & Ghost Stamp.
Next is 1st Edition Thick Stamp with big D Yellow Cheeks, also inside 1st Edition Booster Packs.
The left side of the D, is the same thickness as the left side of the E.
ZAP! Theme Decks with Gold Pull Strip were reprinted to have Shadowless Yellow Cheeks WITHOUT the Ghost Stamp misprint.
You can see it opened here.
There’s at least two more subsequent printings of ZAP! Theme Decks with subtly different packaging, which can both contain Shadowless Yellow Cheeks.
What’s odd, is that both of these package variations were later reprinted containing Unlimited Yellow Cheeks. I can understand switching to Unlimited cards without changing the packaging, but I’m surprised that they’d reprint version 2 of the packaging with Unlimited cards after they’d already switched to version 3 of the packaging.
More info on Theme Deck package versions here.
The last print run of 1st Edition contains 1st Edition Thick Stamp Red Cheeks.
This is packaged with the Thin Stamp holo cards.
You can see it opened here.
If there is a 1st Edition Thin Stamp Pikachu, it will be from this print run, and have Red Cheeks.
Now we switch to Shadowless Booster Packs, which contain Shadowless Red Cheeks Pikachu.
You can see it opened here.
Shadowless Red Cheeks come from booster packs, while Shadowless Yellow Cheeks come from Demo Boosters & Theme Decks.
I haven’t seen Shadowless Yellow Cheeks from Shadowless boosters yet, but maybe it’s possible.
During the E3 Promo print run, they switched from Shadowless Red Cheeks to Unlimited (with shadow) Yellow Cheeks, so both versions exist.
The E3 event didn’t happen until later, but this is when they printed the cards.
Then they printed Unlimited (with shadow) Yellow Cheeks in Unlimited Boosters & more ZAP! Theme Decks.
That should explain when Red Cheeks happened.
While 1st Edition was being sold, someone at WotC decided that Pikachu should have red cheeks. Maybe it was the Art Director, or perhaps a manager told the Art Director to do it.
However it happened, the updated artwork with Red Cheeks was given to the typesetter, who was told to use this for the next print run.
He did that, along with any other changes management had asked for.
When Japan wasn’t happy about the Red Cheeks, there was some finger pointing inside WotC.
The typesetter removed the Red Cheeks at the same time he added the shadow for Unlimited cards, along with whatever other changes they asked him to do.
Redo all of the cards & collation, and replicate the earlier sheet layout.
It seems that Japan being upset about Red Cheeks, is what stopped the Shadowless print run, and also stopped the E3 Promo print run.
The other versions of Pikachu should be easier to put in chronological order.
Here’s a few notes on the international releases.
International English with 1999 copyright was first, because there wasn’t a translation delay.
French, German, Portuguese, & Spanish for Latin America should be July through October.
French 1st Edition started printing September 29th 1999.
I don’t have an exact date for the other languages with 1999 copyright.
Base Set with 2000 copyright date started printing in the UK on November 1st 1999.
Italian, Dutch, & Spanish for Spain have 2000 copyright dates, and should be after November 1st.
Chinese & Korean were last.
They happened in the year 2000.
Chinese started printing in April 2000, not sure about Korean.
You have a beautiful collection!
Best of luck catching them all