You don't use the stock tailshaft, you get it shortened, getting the engine as close to the firewall as possible is very important for you handling.
Any engine that is heavier than the stock one is going to affect your handling, but a compromise can be met.
my sr ke30 has heavier steering, and generally feels less nimble with the 2 litre, but still handles fine,
if i never drove it with the 1300 in it, the handling would not really even get a mention.
Things like longer lower control arms, s13 struts, wrong steering arms will screw your handling soooo much more!