Anywhere the link is referencing a System field like{!User.Id}above will need to be updated to have a dollar sign following the exclamation point like this{!$User.Id}.
Once your URL is doctored up you can throw it into this snippet for the Visualforce page:
<apex:page showHeader="false" sidebar="false"
lightningStylesheets="true"> <div>
<apex:outputLink value="YOUR URL GOES HERE" id="WHATEVER MAKES SENSE">THE DISPLAY NAME OF THE LINK</apex:outputLink>
</div></apex:page>
So your final snippet would look like this:
<apex:page showHeader="false" sidebar="false"
lightningStylesheets="true"> <div>
<apex:outputLink value = "/apex/APXTConga4__Conga_Composer?id={!$User.Id}&QueryId=[ClosedOpps]a1w1a000000Ooo8, [NegotiateOpps]a1w1a000000OooI,[ProposalOpps]a1w1a000000OooN,[CloseLostOpps]a1w1a000000OooS, [OppInfo]a1w1a000000Ooom&TemplateId=a241a000000shZh&DS7=3" id="oppReport">
Conga Opp Report</apex:outputLink> </div></apex:page>
You could wrap any other Custom Links in their own<div>tags to get multiple links on the same page.
Now copy and paste the whole snippet into the body of the VisualForce page, ensuring ‘Available for Lightning Experience, Lightning Communities, and the mobile app’ is checked TRUE. Your page should look something like this:
Once you have your page created it’s time to add it to the homepage! Navigate to your Lightning Home Page click theGear Icon→Edit Page.
From the Lightning App Builder menu, select a Visualforce and drag and drop it onto the page wherever you would like the links to appear.
Give the component a Label, select the Visualforce page you just created and set the Height (75 is ideal if you only have one or two links).
Save your page, activate it and assign to profiles and you’re done!