How do i change the size of a tool?

Improvements

Use GetService() for the Players and StarterPack Services

Use Local Variables for items that are used more than once in your code

Use a Table to store your data rather than different prefixes or datastores

Quick Fix

On Line 54, you are changing the value of the tool in the StarterPack, not the player's Backpack, in order to do this, you'd simply change the line to

local sizer = .5 + (strength.Value / 250)
player:WaitForChild("Backpack"):WaitForChild("Weight")::WaitForChild("Handle").Size = Vector3.new(sizer, sizer, sizer)

Revised Server Script

local serverStorage = game:GetService("ServerStorage")
local datastore = game:GetService("DataStoreService"):GetDataStore("PlayerSave3")

game:GetService("Players").PlayerAdded:Connect(function(player)
	local leaderstats = Instance.new("Folder")
	leaderstats.Name = "leaderstats"
	leaderstats.Parent = player

	local strength = Instance.new("NumberValue")
	strength.Name = "Strength"
	strength.Value = 0
	strength.Parent = leaderstats

	local rebirths = Instance.new("IntValue")
	rebirths.Name = "Rebirths"
	rebirths.Value = 0
	rebirths.Parent = leaderstats

	local dataFolder = Instance.new("Folder")
	dataFolder.Name = player.Name
	dataFolder.Parent = serverStorage:WaitForChild("RemoteData")

	local debounce = Instance.new("BoolValue")
	debounce.Name = "Debounce"
	debounce.Parent = dataFolder

	local success, errormessage = pcall(function()
		datastore:GetAsync(player.UserId)
	end)

	if success then
		local LoadArray = datastore:GetAsync(player.UserId)
		if LoadArray then
			strength.Value = LoadArray[strength.Name]
			rebirths.Value = LoadArray[rebirths.Name]
		end
	else
		warn(errormessage)
	end

	player.CharacterAppearanceLoaded:Connect(function(character)
		local humid = character:WaitForChild("Humanoid")
		local bds = humid:WaitForChild("BodyDepthScale")
		local bhs = humid:WaitForChild("BodyHeightScale")
		local bws = humid:WaitForChild("BodyWidthScale")
		local hhs = humid:WaitForChild("HeadScale")
		local pbw = player:WaitForChild("Backpack"):WaitForChild("Weight"):WaitForChild("Handle")
		
		local default1 = 0.5
		local default2 = 16
		local base = 250
		
		local p1 = default1 + (strength.Value / base)
		local s1 = default2 + (strength.Value / base)
		
		bds.Value = p1
		bhs.Value = p1
		bws.Value = p1
		hhs.Value = p1
		humid.WalkSpeed = s1
	
		strength:GetPropertyChangedSignal("Value"):Connect(function()
			local p2 = default1 + (strength.Value / base)
			local s2 = default2 + (strength.Value / base)
			
			bds.Value = p2
			bhs.Value = p2
			bws.Value = p2
			hhs.Value = p2
			pbw.Size = Vector3.new(p2, p2, p2)
			humid.WalkSpeed = s2
		end)
	end)
end)

game:GetService("Players").PlayerRemoving:Connect(function(player)
	local lead = player:WaitForChild("leaderstats")
	local str = lead:WaitForChild("Strength")
	local reb = lead:WaitForChild("Rebirths")
	
	local SaveArray = {}
	SaveArray[str.Name] = str.Value
	SaveArray[reb.Name] = reb.Value

	local success, errormessage = pcall(function()
		datastore:SetAsync(player.UserId, SaveArray)
	end)
	
	if not success then
		warn(errormessage)
	end
end)