I would not comment on the difficulty of the course. Having a 800 Math SAT II score and a 5 on the AP Calculus exam basically speaks for itself that you are no slouch in Math. Since the UC’s do not accept counselor recommendations, I would not address this issue yourself.
UC’s will review your application as a whole so if you have done well with your other courses, a few outliers will not be as significant as a downward trend. For UCSC and UCR, you look solid. Best of luck.
2018 Freshman admit rates for UC GPA of 3.80-4.19 capped weighted and not major specific:
UCB: 10%
UCLA: 9%
UCSD: 34%
UCSB: 38%
UCD: 41%
UCI: 38%
UCSC: 70%
UCR: 84%
UCM: 95%
2019 UC capped weighted GPA averages along with 25th-75th percentile range:
UCB: 4.23 (4.15-4.30)
UCLA: 4.25 (4.18-4.32)
UCSD: 4.16 (4.03-4.28)
UCSB: 4.16 (4.04-4.28)
UCI: 4.13 (4.00-4.25)
UCD: 4.13 (4.00-4.26)
UCSC: 3.96 (3.76-4.16)
UCR: 3.90 (3.69-4.11)
UCM: 3.73 (3.45-4.00)
2019 Data:
25th - 75th percentiles for SAT totals:
UCB: 1340-1540
UCLA: 1330-1550
UCSD: 1300-1520
UCSB: 1280-1520
UCD: 1230-1490
UCI: 1250-1510
UCSC: 1200-1450
UCR: 1130-1400
UCM: 1020-1290