Regarding PW, since you cannot possibly have it outside of
a JC, simply declare this on your Uni application.
Depending on the Uni and course involved, you may (or may
not, depending on the course and Uni) be at a disadvantage compared
to other applicants. But honestly, a little thing like PW shouldn't
deter you from taking A levels as a private candidate.
Next, regarding Chemistry, you should take it as a H2 subject,
no doubt about it. H2 Chem is extremely useful and necessary for
many Uni Science courses, while H1 Chem is utterly useless as a
prerequisite for these Uni Science courses.
Lastly, since NUS requires GP and the 3 H2 subjects to be taken
in 1 sitting, obviously you should retake all these subjects at
least twice, in 2013 and again in 2014, or even a 3rd time in 2015,
if that's what it takes to get decent grades (eg. AABB).
For your self-study, you may find my recommend lists
of Chemistry resources (both books and websites) helpful :
http://infinity.usanethosting.com/Tuition/#Books_for_H2_Chemistry
http://infinity.usanethosting.com/Tuition/#H2_Planning_and_other_goodies
