im in the middle of a conversion myself on my 1.3 mk4 bonus...

a 1.6 cvh carbed engine will go straight in on the same mounts..

1.8 zetec (what im going for i think) goes straight in but needs the rear engine mount (i think) modding a little bit..

you can change to injection, but you will need the injection tank etc etc..

about the brakes...you can change to rs turbo brakes which will go straight onto the standard hubs....

or cosworth brakes..which i picked up last night and will be fitting the weekend!