Trimethoprim are basically sulphonamides and they do have a reputation for the side effects that you have mentioned.
Certainly blood and protein in the urine is something that does need investigating by a Urologist. It may well be associated with a single urinary infection, but she has had multiple urinary infections and a renal stone, which makes further specialist investigation a priority.
Abnormalities causing recurrent urinary tract infections may be lurking in the bladder, ureter or kidneys.