My process is similar, though I am comparing my ledger, which contains a mixture of manual and converted bank data, with the bank's online statement. I compare the daily balances, which I get with eg:
hledger register -p 'daily to today' -d 'd>=[last month]' 'wells fargo:checking' Starting from the last point of agreement, I go day by day and investigate any discrepancies. Usually I will make each day's balance match exactly, by correcting any mistakes and adding actual/effective dates if needed (http://hledger.org/MANUAL.html#actual-effective-dates).
