Hi Clay,
I used to use a spreadsheet, but since it was set up for the flat rate VAT scheme (and you don't want to go there), it's not going to be all that helpful.
As a serious question, how much do you value your time? I use
Free Agent for farm accounts (not because it's particularly suited to a smallholding, but because I also use it elsewhere, so it just made sense). I pay roughly £15 a month, and get automatic invoicing, a connection to my bank account, a mobile app for recording expenses and mileage, and a dial-in so my accountant can access everything without me having to send files back and forth. It also does all my VAT calculations for me, reminds me when a VAT return is due, and files it with a single click.
Sure, I could do all that using a spreadsheet, but I've got more interesting things to do with my time - haven't you?