Hi there. Long-time Virginia landlord and property manager here. I can shed some light.
LAW EXEMPTIONS - There are very few parts of the VRLTA that allow an exemption for people based on units owned, and late fees is not one of them. You are exempt from the "source of income" protection though, which means you are allowed to deny an application just because they have a housing choice voucher, which would not be the case if you owned more than 4 units. The law now also requires landlords with more than 3 properties to give at least a 60 day notice of termination. If you own 3 or less, which you do, you are exempt from this and can offer a 30 day notice of termination. (Note - No tenants will be sucessful moving with only 30 days notice in this market. I recommend you stick with 60 if you want to avoid issues.)
LATE FEES - The max late fee you can charge is the greater of 10% of one month rent or the balance owed. Your lease cannot charge a higher fee. If the tenant pays half of the rent on-time, you can only charge 10% on the remaining balance. Your $25/day lease clause is not legal or enforcable.
GRACE PERIOD - You are reading the law wrong here. It is a common mistake. The VRLTA does not require you have a grace period. My rent is due on the first, late on the second. What it does say is IN ABSENCE OF A WRITTEN LEASE, the late fee is 10% with a 5 day grace period.