This shows a general approach to easing the human-error potential in step 3 and 4 covered at http://commercesdn.sitecore.net/SitecoreCommerce/DeploymentGuide/en-us/index.html#Concepts/c_M_ChangesToDefaultSettings.html

ConfigureSitecoreCommerceJSON.ps1

<#
Author: Grant Killian
Created Date: Sept 1, 2017
Ease the human-error potential in step 3 and 4 covered at http://commercesdn.sitecore.net/SitecoreCommerce/DeploymentGuide/en-us/index.html#Concepts/c_M_ChangesToDefaultSettings.html 
For repetitive installs, it's a pattern that can be used to update a site name etc, too.  Here I focus on the SQL Server and Sitecore credentials but other settings could be updated too (just be certain you have the right pattern to match/replace).
#>

$dbServer ="your db server" #for Azure SQL, something like "qa2-proj-sql.database.windows.net,1433" is what you'd use
$dbuser ="SQLuser"
$dbpwd = "secret"

$CFSolutionStorefrontSite_profilesName = "CFSolutionStorefrontSite_profilesRenamed"
$CFSolutionStorefrontSite_productcatalogName = "CFSolutionStorefrontSite_productcatalogRenamed"
$SitecoreCommerce_SharedEnvironmentsName = "SitecoreCommerce_SharedEnvironmentsRenamed"
$SitecoreCommerce_GlobalName = "SitecoreCommerce_GlobalRenamed"

$scuser = "admin"
$scpwd = "secret"
$theRoot = "S:\Sitecore"

########################### shouldn't have to touch anything below here ########################### 

function updateEnvJSONFile($theFile)
{
    #in all of these, the white space is critical and note there are 2 spaces between the ":" and the value, typically
     
    $original="`"UserName`":  `"`"," # $key here that it's a "blank" pwd as there is a sitecore username here too that is not the same value
    $updated="`"UserName`": `"$dbuser`","
    (Get-Content "$theFile").Replace($original, $updated) | Set-Content "$theFile.new"

    $original="`"Password`":  `"`","  
    $updated="`"Password`": `"$dbpwd`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"
 
    $original="`"Server`":  `".`","  
    $updated="`"Server`": `"$dbServer`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"

    $original="`"TrustedConnection`":  true,"  
    $updated="`"TrustedConnection`":  false,"
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"

    $original="`"UserName`":  `"admin`","  
    $updated="`"UserName`": `"$scuser`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"
    
    $original="`"Password`":  `"b`""  
    $updated="`"Password`": `"$scpwd`""
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"

    <# every json file references these three databases by name only:
    "Database":  "CFSolutionStorefrontSite_profiles",
    "Database":  "SitecoreCommerce_SharedEnvironments",
    "Database":  "CFSolutionStorefrontSite_productcatalog",
    #>
    
    $original="`"Database`":  `"CFSolutionStorefrontSite_profiles`","
    $updated ="`"Database`":  `"$CFSolutionStorefrontSite_profilesName`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"
    
    $original="`"Database`":  `"SitecoreCommerce_SharedEnvironments`","
    $updated ="`"Database`":  `"$SitecoreCommerce_SharedEnvironmentsName`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"
    
    $original="`"Database`":  `"CFSolutionStorefrontSite_productcatalog`","
    $updated ="`"Database`":  `"$CFSolutionStorefrontSite_productcatalogName`","
    (Get-Content "$theFile.new").Replace($original, $updated) | Set-Content "$theFile.new"
}

function updateGlobalFile()
{
$jsonGlobal = "$theRoot\CommerceAuthoring\wwwroot\bootstrap\Global.json"

$original="`"Database`": `"SitecoreCommerce_Global`","
$updated="`"Database`": `"$SitecoreCommerce_GlobalName`","
(Get-Content $jsonGlobal).Replace($original, $updated) | Set-Content "$jsonGlobal.new"

$original="`"Password`": `"`","
$updated="`"Password`": `"$dbpwd`","
(Get-Content "$jsonGlobal.new").Replace($original, $updated) | Set-Content "$jsonGlobal.new"

$original="`"Server`": `"`.`","
$updated="`"Server`": `"$dbServer`","
(Get-Content "$jsonGlobal.new").Replace($original, $updated) | Set-Content "$jsonGlobal.new"

$original="`"UserName`": `"`","
$updated="`"UserName`": `"$dbuser`","
(Get-Content "$jsonGlobal.new").Replace($original, $updated) | Set-Content "$jsonGlobal.new"

$original="`"TrustedConnection`": true,"
$updated="`"TrustedConnection`": false,"
(Get-Content "$jsonGlobal.new").Replace($original, $updated) | Set-Content "$jsonGlobal.new"
}

$json1 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.AdventureWorks.CommerceAuthoring-1.0.0.json"
$json2 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.AdventureWorks.CommerceMinions-1.0.0.json"
$json3 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.AdventureWorks.CommerceShops-1.0.0.json"
$json4 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.Habitat.CommerceAuthoring-1.0.0.json"
$json5 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.Habitat.CommerceMinions-1.0.0.json"
$json6 = "$theRoot\CommerceAuthoring\wwwroot\data\Environments\PlugIn.Habitat.CommerceShops-1.0.0.json"

updateGlobalFile

updateEnvJSONFile $json1
updateEnvJSONFile $json2
updateEnvJSONFile $json3
updateEnvJSONFile $json4
updateEnvJSONFile $json5
updateEnvJSONFile $json6