I just spent a while sorting this out, so I'm posting it on the chance that it may be helpful for someone else.
To do end-of-year accounts for our organisation, we needed to reconcile our sales records with our paypal account records, and also to gather information about VAT (tax) charged.
Our sales channels include: Ubercart, Email, Phone and a Physical Shop.
For EACH of those sales channels, we receive payments coming in through Paypal as well as other types of payments (e.g. cash, cheque)
So that means that our Paypal transactions include Ubercart and non-Ubercart payments.
So what I wanted to do was to identify which Paypal payments are Ubercart sales, and to get the Ubercart order number and VAT (tax) charged for each of those (I'm using VAT module and the tax value is sent to Paypal).
So the first problem was that Paypal's standard reports don't include things like order numbers and tax. My History menu tab at the top of my Paypal screen doesn't give me the option of downloading a CSV, but digging around I found this. I can't remember the exact route I used to get there, but the url is: https://history.paypal.com/ie/cgi-bin/webscr?cmd=_history-download It's pretty straightforward from there.
This Paypal export includes EVERYTHING, including columns for: Paypal transaction ID , Invoice number (which includes Ubercart order ID as part of it) and Sales Tax (VAT in my case).
To match up Ubercart Paypal orders you can use the Invoice number column fromthe Paypal export, which is in a format like 402-1253100479. The numbers before the dash (402 here) seem to consistently be the Ubercart invoice number.
Another more certain way to match up records is to use the Paypal Transacation ID, which also appears in the Paypal export. You can get a list of these from Ubercart with a simple query like SELECT order_id,txn_id FROM `uc_payment_paypal_ipn`
Then you can take the result of that query and paste it into your Paypal export spreadhseet, and use the spreadshsheet lookup function (eg VLOOKUP) so that for each Paypal transaction you can get the corresponding Ubercart order number.
Hope this is useful to someone 