Hey,
I'm Alex, full stack dev. Did you tried to play around taxes via the magento admin panel? I fixed one Magento store taxes last week as they got system which calculates VAT wrong or doesn't add shipping price, and many other bugs. All I done is played around Magento administration dashboard.
Your given bugs seems to be related with magento taxes/prices settings, I might look and test something if you're interested but I can't guarantee I can fix it as this is a complex problem.
Would also need to double check paypal gateway.
Anyway, I can lookup.
Cheers
Alex