This script needs some massive cleanup. Short, easy-to-understand code is good code. It's also code that has fewer bugs.

Naming

ROBLOX now uses the convention that methods on objects should be :PascalCase(). That is, :FindFirstChild instead of :findFirstChild(), and :Destroy() instead of :destroy(), :Remove() instead of :remove(). This isn't mandatory (though it might be one day), but it's ROBLOX's preferred style.

Use meaningful, human-readable names! player instead of p!

Conditions

It's not idiomatic to use () around a condition in Lua. It's unnecessary messiness.

It's not idiomatic to use ~= nil. You can just use if tool then.

Similarly, instead of if tooleq.Value == false then, it's much easier to read and interpet if not tooleq.Value then. You should probably use a better name than tooleq so it actually reads like a human would write it, e.g., if not equipped.Value then.

You can make it even easier to understand by flipping the then and else blocks, so that the conditions reads if equipped.Value then -- negatives are harder to understand.

Functions

The function TransformModel doesn't belong in the middle of three ifs and an event connection. You want to define functions separately as much as possible.

A good illustration of why you want that is in this script. You've repeated TransformModel twice.

Move it out.

Spacing

pairs is a function. Standard spacing rules suggest you should use pairs(decs) not pairs (decs).

You should have spaces after commas. _, v instead of _,v.

Don't Repeat Yourself!

Repeating yourself is bad. It means you have more code that you have to understand.

It also means if you have a bug in one place, you have a bug everywhere you copy-pasted.

Don't copy-paste code. Don't repeat yourself.

Lines 7 to 52 are repeated -- they are almost exactly the same. Only the different parts should be "repeated" -- lines 18+ are exactly the same.

It could instead look like this:

            local model = Instance.new("Model")
            model.Name = "Case"
            local newcase
            if equipped.Value then
                newcase = game.ServerStorage.Case:Clone()
                newcase.Handle.BrickColor = tool.Handle.BrickColor
                local tool = player.Backpack:FindFirstChild("Case")
                if tool then
                    tool:remove()
                end
            else
                newcase = tool
            end
            local decs = newcase:GetChildren()
            for _, v in pairs(decs) do
                if v:IsA("BasePart") then
                    v.Parent = model
                    v.Anchored = true
                    v.CanCollide = true
                end 
            end
            newcase:Destroy()

However this code is not right: newcase:Destroy() would nullify all of the work done to create newcase and set its children's properties.

I'm guessing that is a typo.

You're shadowing local tool in this code. It's not even necessary, since it's the same as the old tool. Again, don't repeat yourself.

The :Destroy() is similarly redundant, since you'll handle it with newcase:Destroy() in this rewrite.

Rewritten

function TransformModel(objects, center, new, recurse)
    for _,object in pairs(objects) do
        if object:IsA("BasePart") then
            object.CFrame = new:toWorldSpace(center:toObjectSpace(object.CFrame))
        end
        if recurse then
            TransformModel(object:GetChildren(), center, new, true)
        end
    end
end

script.Parent.ClickDetector.MouseClick:connect(function(player)
    local tool = player.Backpack:FindFirstChild("Case")
    if tool then
        local equipped = tool:FindFirstChild("EquippedV")
        if equipped then
            local model = Instance.new("Model")
            model.Name = "Case"
            local newcase
            if equipped.Value then
                newcase = game.ServerStorage.Case:Clone()
                newcase.Handle.BrickColor = tool.Handle.BrickColor
            else
                newcase = tool
            end
            local decs = newcase:GetChildren()
            for _, v in pairs(decs) do
                if v:IsA("BasePart") then
                    v.Parent = model
                    v.Anchored = true
                    v.CanCollide = true
                end 
            end
-----------------------------------------------------------------------------
            newcase:Destroy() -- Something's not right here
-----------------------------------------------------------------------------
            model.Parent = game.Workspace
            model:MoveTo(script.Parent.Position)

            local center = model:GetModelCFrame()
            TransformModel(
                model:GetChildren(),
                center,
                center * CFrame.Angles(0, math.rad(90), math.rad(90)),
                true
            )

            local cd = Instance.new("ClickDetector")
            cd.Parent = model
            local tags = script.Parent.AddTag:Clone()
            tags.Parent = model
            tags.Disabled = false
            local welds = script["Weld 2.1"]:Clone()
            welds.Parent = model
            welds.Disabled = false
            script.Parent.ClickDetector.MaxActivationDistance = 0
            script.Parent.Transparency = 1
            wait(15)
            script.Parent.ClickDetector.MaxActivationDistance = 32
            script.Parent.Transparency = 0.8
        end
    end
end)