Concerned High School Junior; Boston University Engineering

Hey guys, asking here as I'm a Junior, soon to be applying to colleges, from Texas. I am aspiring to be a Mechanical Engineer, with a specialization in Aerospace. Sadly, my Freshman year of high school went horribly, as I had a hard time acclimating to high school, and my grades suffered from it. Although Sophomore and Junior years have been very good so far (All B's and A's), I'm afraid my Freshman year grades will affect my chances drastically. 
My GPA is 5.6857 out of 6.5714 (my school uses a weird scale), which equates roughly to 3.46, weighted GPA, only factoring in core classes. I am at the edge of the third quartile out of 627 students, and have taken 3 AP courses this year, and will be taking 5, possibly 6, next year. My SAT scores are decent, but I know for a fact I can do better, and will be taking it again over the summer. Not sure if it is worth taking the ACT.

TEST 1: READING: 700 MATH: 580 WRITING: 650
TEST 2: READING: 700 MATH: 620 WRITING: 620
I do realize I am at the tail-end of the applicant pool, and what would you guys suggest I do to make me more appealing to this school?
Not sure if this matters, but I have also participated in several leadership programs over the past summer’s (People to People, Envision, ID Tech) and have started 2 clubs at my school (Car Club and Aerospace/Aeronautical Club), while also participating in multiple other clubs/community service. I am applying to NTHS next year, and possibly NHS, though I doubt I will be accepted, as the cutoff GPA is 5.9000 (3.59), although there have been exceptions to this rule in the past.
I also will most likely be taking Chem II AP next year, rather than Physics C or Physics II AP; I hope this does not lessen my chances of admission.

I do apologize for the wall of text, but I hope to hear back from someone on here, you guys seem so knowledgeable. I just hope I didn’t jeopardize my college chances due to my below-par freshman year, and I’m hoping my hard work posterior to that year will pay off.

Thanks so much to any that can help me out!

I just answered this in the other thread-take the SAT2s and ACTs. Those math scores are abysmal if you want engineering.

Why???

Are you being serious? I’ve been told that they are around the average for most students applying as engineers at A&M when I spoke to one of the admissions counselors there. They gave me the impression that those scores were good.

I didn’t think it would be that much of a difference at BU

I can’t take the other users’ posts seriously. Your SAT score for math is below average for math and writing, but that does not mean you won’t get in. I was accepted in the college of engineering last year with a math score of 650, so it really depends on the rest of your application. If you can improve it, try to, but don’t take the SAT more than 3 times.