You can't do a transfer mid year as it's not internal. You need to apply with UAC near the end of the year.
As for specific subjects, I can only comment on what I did through flexible. In first semester it was ENGG1800 (Intro to eng discipline) and ENGG1801 (Eng computing), and ENGG1802 (Mechanics). However mechanics can be substituted with PHYS1001, check with department for specific details.
For both semesters you need your 12cp of maths. In semester one, try to do ENGG1800 and ENGG1801 (if you can't do the latter, don't worry, combined people are known to take it in second year). I did chem, you might be alright with just doing physics but check with department. I think what you'll be doing will not be up to course requirement but Doug might waive it. For second semester, if you do physics in first semester there's no need to do mechanics.
As for the other subjects listed on the website, I'm not sure whether I didn't do the combined exempt units because I was combined, or because I was flexible. Again it's best to check with department. For ENGG1803 (Professional), I was exempt, but I'm not sure why I was exempt.
If you do my combination (ENGG1800, 1801, 1802/PHYS1001) and one of chemistry or physics in both semesters, and obtain a D average, I'm pretty sure any shortcomings will be waived. You might lose a few electives later on but you will definitely finish without delay.
If you choose to do combined, the above combination will definitely work (well, it did for me).
As for mechanics vs physics, I recommend physics because you need to do 36cp of junior science for BSc, and if you do combined you can get that out of the way without using up 2nd year electives to finish your 1st year science requirements.