Does anyone happen to know if the custom tokens that Team Covenant makes are tourney legal? Are there any that would not be? I'd like to figure this out before I invest in any of them.

This is from the Tournament Rules

Quote

Tokens
Tokens are representations of information about the game or game state. The presence of tokens—other than tokens that are essential components—is marked by one or more indicators. Indicators may also be used to represent multiple tokens, or other open or derived information. Essential tokens are ship and obstacle tokens, as well as any bomb tokens (in a reasonable quantity) required for a player’s list. Other tokens are not essential components.
Typically, players use the cardboard tokens included in official product as indicators. However, players may choose to use other items as indicators, so long as they do not obscure significant component information, are resistant to accidental modification, and their purpose of use is clear to both players. The marshal is responsible for determining the legality of an indicator and its reasonable usage during a match if objected to by its owner’s opponent.

The after-market tokens used for evade , focus , target lock , stress , cloak , etc are all perfectly legal as long as their function is clear and are considered "Indicator" tokens. Any after-market ship , obstacle or bomb tokens should be checked by the TO beforehand if you're unsure, as these are "Essential" tokens and really should be FFG originals.