**My first question is: I assume that 32% is multiplied on someone's ***base *shield capacity (1300 for Scout, 1500 for Bomber, 1800 for Strike). I assume it is not affected by other bonuses to shield capacity, such as Large Reactor. Is that true?

Correct - this is always based on percent of base.
**My second question is: Assuming my first assumption is true, whose shield capacity is that 32% multiplied on for my allies? Is it multiplied by my own ship's base shield capacity, or the base shield capacity of the ally being healed?**

It is based on the base shield capacity of each ally being healed.
Same question goes for the percent listed in the two T3 upgrade options:

The first tick of the Shield Projector effect restores an additional 8% shield power.

Ability duration is increased by 4 seconds, restoring an additional 16% shield strength.

Thanks!

These are all percent of base. It's safe to assume when it comes to shields, we'll base everything off of the base value. That way we don't get into any edge cases with percent of a percentage, or trying to apply an effect when your current shields are at 0 or are boosted. This way, boosts are predictable, calculable numbers.

Hope that helps!