Originally Posted by bign
I'm noticing on some of the satire bikes they either run a shift kit or jack shaft set up to fix the chain alignment issues
These things are possible but the ease of installing them and having them work correctly is dependent on your skills. Another option is an off-set engine which requires custom fabricated mounts.
I have to agree with crassius in that for a first bike project you might be better off to keep things simple, learn what works and what doesn't and save the more ambitious strategy for your next build. Not trying to stifle your dreams and we have no idea about your mechanical abilities so we're just offering opinions.