What happened to you is common and has a name: the gap between the loan estimate and the closing disclosure. The loan estimate (LE) is the standardized form a lender must give you within three business days of application. The closing disclosure (CD) is the final version, due to you at least three business days before closing. Comparing those two documents line by line is the reconciliation moment you are looking for.
The per diem issue you ran into is one of the trickier line items. Per diem interest is the daily interest charged from closing day through the end of that month. It shifts every time your closing date moves, so a two-week slip can add real money. On a $200,000 loan at 7%, that is roughly $38 per day. Ten days of drift is $380 you did not plan for.
Here is what I would do differently for the Henrico deal. When you get the loan estimate, ask your broker to show you exactly how the origination fee is calculated and whether it is a flat fee or a percentage of the loan. Then ask the lender the same question in writing. You want both answers referring to the same loan amount and the same closing date. If the answers look different, that is the moment to resolve it, not at the table.
When the closing disclosure arrives, give yourself the full three days to read it against the loan estimate. The CFPB publishes a free side-by-side guide showing which fees can change and by how much. That is worth pulling up.
One thing worth confirming with a real estate attorney in Virginia: whether any of your closing costs fall under protections that limit how much certain fees can increase from LE to CD. A local attorney can answer that in about ten minutes.
What loan type are you using for this bungalow, conventional or something else?