More likely than a side effect of acyclovir, you probably are experiencing neuropathy from the HSV infection, causing partial bladder paralysis or other neurological dysfunction of the lower urinary tract. Many cases of initial genital herpes are associated with such localized neurological side effects. And yes, the initial outbreak of herpes can have a stuttering course that lasts up to 3-6 weeks; not commonly, but it happens. In general, acyclovir and its relatives (valacyclovir, famciclovir) are very safe and have almost no side effects, and I certainly have never heard of anything like this due to the drug. Whether or not due to acyclovir, your symptoms suggest lower urinary tract obstruction, not kidney damage. Mostl likely you need more acyclovir, not less--or perhaps a switch to valacyclovir, which gives better blood levels of the drug than acyclovir. But your provider needs to make the decision; no online expert can make a definite diagnosis from afar, and I also cannot be responsible for any treatment decisions.
I hope this helps. Best wishes-- HHH, MD