If you want honesty, with a weighted GPA of 3.63 and an SAT score of 1380/ACT of 29, you have an uphill battle to get your application seriously considered.
Compare you stats to the stats of last year’s incoming class and you will get a reality check. Also your counselor is wrong in that your SAT scores are good enough so you do need to take some Subject test scores since you need all the help you can get to be a viable candidate for a school like Stanford.
From the Stanford Website and Common Dataset:
Middle 50% Test Scores:
SAT Evidence-Based Reading and Writing: 690-760
SAT Math Section: 700-780
ACT Composite: 32-35
Average Unweighted GPA: 3.94
Stanford is a Reach school for all applicants due to the sub 5% acceptance rate and anyone that tells you it is not, does not know what they are talking about.