#linked abilities

No. First of all, Sword of Kaldra is what's exiling the creatures dealt damage by Lumbering Battlement, not the creature itself. More importantly, however, is the fact that Lumbering Battlement's last ability is linked to its exile ability and will only count the cards exiled by that ability and not cards exiled by any other abilities it might gain.

X will be equal to the combined power of the two exiled cards because of this rule:

607.3 If, within a pair of linked abilities, one ability refers to a single object as “the exiled card,” “a card exiled with [this card],” or a similar phrase, and the other ability has exiled multiple cards (usually because it was copied), the ability refers to each of the exiled cards. If that ability asks for any information about the exiled card, such as a characteristic or converted mana cost, it gets multiple answers. If these answers are used to determine the value of a variable, the sum of the answers is used. If that ability performs any actions on the exiled card, it performs that action on each exiled card.

Mairsil doesn’t have Riptide Replicator’s “choose a color and creature type” ability. When Mairsil uses Riptide Replicator’s ability, there’s no color or type chosen and so the token will be colorless with no creature types.

No.

Bomat Courier’s activated ability is linked to its triggered ability. The activated ability can only ever put cards into your hand that were exiled by the attack trigger.

This still holds when Mairsil gains Bomat Courier’s activated ability. Since he doesn’t also gain the attack trigger, this means that the gained Bomat Courier ability will never be able to put any cards into your hand.

This doesn’t work.

Sisters of Stone Death’s last ability specifically looks for cards in exile and the commander isn’t exiled. This differs from the Oblivion Ring situation because SoSD’s ability is referring to a class of cards, not a specific card and so its last ability doesn’t track individual cards like Oblivion Ring’s abilities do.

The main way that you’d know that each Bomat Courier tracks its own cards is the wording of the activated ability, specifically the phrase “cards exiled with Bomat Courier”.

When a card refers to itself by name this way, it just means itself and not any other card with the same name. If you were going to just pool all the Bomat Courier cards together, then the ability would refer to “cards exiled with cards named Bomat Courier”. (We saw this sort of templating for the first time in Conspiracy: Take the Crown on Arcane Savant, Caller of the Untamed, and Volatile Chimera.)

Also, Bomat Courier’s triggered and activated abilities are a pair of linked abilities, and so the activated ability can only ever access cards exiled by that triggered ability and not any other cards it might exile through other shenanigans. And because of these linked abilities, there’s no way for one Bomat Courier to access cards exiled by another Bomat Courier.

When Prototype Portal enters the battlefield, its Imprint ability will trigger twice, and you can exile an artifact card from your hand for each of the triggers. But that’s the easier part that anyone could figure out...

So what happens if you want to activate that “X, T” ability? Well... the good news is you’ll get to make a copy of both of the exiled cards. The bad news is that you have to pay the total combined CMCs of the two cards to do so. (This is because Prototype Portal gets two answers when it determines the CMC of the exiled cards and then uses a combined value.)

For example, if you imprinted a Bronze Sable (CMC 2) and a Trading Post (CMC 4) on the Prototype Portal, the cost to activate the second ability is 6 and you’ll get a token Bronze Sable and a token Trading Post when the ability resolves.

As soon as Endless Horizons leaves the battlefield, the plains it fetch are stranded in exile. Even if you return it to the battlefield it’s a different object from the one whose trigger exiled those plains. You’ll have to find some new plains to exile.