You need to contact admissions and talk to them. You have to include your sr courses on your transcript, so alg 2 and physics would be on your transcript as planned for spring. But, the issue you have to face is the competitiveness of admissions. You need to look at the freshman profiles for the different schools. If engineering is a more competitive admit, your transcript is going to be weak.
Do you have standardized test scores? Subject test scores? As a homeschool student, your test scores are going to carry more weight than grades.