Keep in mind I'm not a programmer, and anything I know about Lua I learned in the past hour, so there's probably a much better way to do this.

With that said, I edited the encounter.lua like this:

-- A basic encounter script skeleton you can copy and modify for your own creations.

-- music = "shine_on_you_crazy_diamond" --Always OGG. Extension is added automatically. Uncomment for custom music.
encountertext = "Poseur strikes a pose!" --Modify as necessary. It will only be read out in the action select screen.
nextwaves = {"bullettest_chaserorb"}
randomwave = 1
wavetimer = 1.0
arenasize = {155, 130}
enemypositions = {
{0, 0}
}

-- A custom list with attacks to choose from. Actual selection happens in EnemyDialogueEnding(). Put here in case you want to use it.
possible_attacks = {"bullettest_bouncy", "bullettest_chaserorb", "bullettest_touhou"}

function EncounterStarting()
    -- If you want to change the game state immediately, this is the place.
end

function EnemyDialogueStarting()
    -- Good location for setting monster dialogue depending on how the battle is going.
end

function EnemyDialogueEnding()
    -- Good location to fill the 'nextwaves' table with the attacks you want to have simultaneously.
    -- This example line below takes a random attack from 'possible_attacks'.
    randomwave = math.random(1, 3)
    if randomwave == 1 then
        wavetimer = 4.0
        nextwaves = {"bullettest_bouncy"}
    elseif randomwave == 2 then
        wavetimer = 2.0
        nextwaves = {"bullettest_chaserorb"}
    elseif randomwave == 3 then
        wavetimer = 10.0
        nextwaves = {"bullettest_touhou"}
    end

    --nextwaves = { possible_attacks[math.random(#possible_attacks)] }
end

function DefenseEnding() --This built-in function fires after the defense round ends.
    encountertext = RandomEncounterText() --This built-in function gets a random encounter text from a random enemy.
end

function HandleSpare()
    BattleDialog({"Sparing functionality\ris still broken.\nSorry!"})
end

function HandleItem(ItemID)
    BattleDialog({"Selected item " .. ItemID .. "."})
end

The only changes I made were adding randomwave = 1 to the top, adding in

randomwave = math.random(1, 3)
if randomwave == 1 then
    wavetimer = 4.0
    nextwaves = {"bullettest_bouncy"}
elseif randomwave == 2 then
    wavetimer = 2.0
    nextwaves = {"bullettest_chaserorb"}
elseif randomwave == 3 then
    wavetimer = 10.0
    nextwaves = {"bullettest_touhou"}
end

to the function EnemyDialogueEnding(), and removing the original wave randomizer.

This makes it so you can change the individual wave times. Right now, I have it set up so the bouncy bullets lasts for 4 second, chaser orb lasts for 2 seconds, and Touhou bullets lasts for 10 seconds.