How to Cycle through 8 bricks, making 2 transparent every time?

Your if statements within lines 17-30 are not checking for the right conditions. In each if statement, you want to check if a part is transparent, and also if the part after that is not transparent.

You are just checking if they are transparent, which will cause the script to run a scope without checking the other statements.

Fixed Code:

debounce = false
Tool = script.Parent
local player = game.Players.LocalPlayer
repeat wait() until player.Character ~= nil
local hum = player.Character:WaitForChild("Humanoid")

local animation = script.EatingAnimation 
local animation2 = script.HoldingAnimation 
local AnimTrack = hum:LoadAnimation(animation) 
local AnimTrack2 = hum:LoadAnimation(animation2)

Tool.Equipped:connect(function(mouse)
    if player:IsInGroup(2608221) then   
        AnimTrack2:Play()
    end
    mouse.Button1Down:connect(function()
        if debounce == false then    
            debounce = true
            if Tool.SR1.Transparency == 0 then
                Tool.SR1.Transparency = 1
                    Tool.SR11.Transparency = 1
                AnimTrack:Play()
            elseif Tool.SR1.Transparency == 1 and Tool.SR2.Transparency == 0 then
                    Tool.SR2.Transparency = 1
                    Tool.SR22.Transparency = 1
                AnimTrack:Play()
            elseif Tool.SR2.Transparency == 1 and Tool.SR3.Transparency == 0 then 
                    Tool.SR3.Transparency = 1
                    Tool.SR33.Transparency = 1
                AnimTrack:Play()
            elseif Tool.SR3.Transparency == 1 and Tool.SR4.Transparency == 0 then
                    Tool.SR4.Transparency = 1
                    Tool.SR44.Transparency = 1
                AnimTrack:Play()
                end
            wait(2.1)
            debounce = false
        end
    end)
end)

Tool.Unequipped:connect(function()
    AnimTrack:Stop()
    AnimTrack2:Stop()
end)

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I believe the problem lies within your conditionals on lines 17-30. You don't end the first one until line 33 which might not be what you want. Also, you were checking to see if SR2 and SR22 were transparent after making them transparent so it would've ran on the first try anyway. The way the script works now is it checks to see which is the highest number of transparent bricks and then makes the next higher one transparent.

debounce = false
Tool = script.Parent
local player = game.Players.LocalPlayer
repeat wait() until player.Character ~= nil
local hum = player.Character:WaitForChild("Humanoid")

local animation = script.EatingAnimation 
local animation2 = script.HoldingAnimation 
local AnimTrack = hum:LoadAnimation(animation) 
local AnimTrack2 = hum:LoadAnimation(animation2)

Tool.Equipped:connect(function(mouse)
    if player:IsInGroup(2608221) then   
        AnimTrack2:Play()
    end
    mouse.Button1Down:connect(function()
        if not debounce then   
            if Tool.SR4.Transparency ~= 1 and Tool.SR44.Transparency ~= 1 then 
                AnimTrack:Play()
            end
            debounce = true
            if Tool.SR3.Transparency == 1 or Tool.SR33.Transparency == 1 then
                Tool.SR4.Transparency = 1
                    Tool.SR44.Transparency = 1
            elseif Tool.SR2.Transparency == 1 or Tool.SR22.Transparency == 1 then 
                    Tool.SR3.Transparency = 1
                    Tool.SR33.Transparency = 1
            elseif Tool.SR1.Transparency == 1 or Tool.SR11.Transparency == 1 then
                    Tool.SR2.Transparency = 1
                    Tool.SR2.Transparency = 1
            else
                    Tool.SR1.Transparency = 1
                    Tool.SR11.Transparency = 1
            end
            wait(2.1)
            debounce = false
        end
    end)
end)

Tool.Unequipped:connect(function()
    AnimTrack:Stop()
    AnimTrack2:Stop()
end)