I  have been  trading  for  quite a few  years... I have  been  using the   first in ; first  out method   for  Capital  gains... The  acb  is a  moving  target  if  you are  buying  and  selling   frequently.... Using  an ACB  means  there  will be  a spreadsheet for  every  stock... the   average   will  change  every   year  as  trades  move  this  arround....  just  too  darn complicated  to   keep track of   40 or  50   different  stocks acb.

Now I  have  not  run into  any  problems  doing  this  method  ... using the  first  in   first  out...  to  make it  easier I   trade   egual  lots ( buys and  sells)  so I  can   staple the  completed  transaction  together as a  unit... If  CRA  decide they  want  to  go the  acb  route...  I  have  one  heck of a  pile  of  trades  for them  to   run their   numbers  on.... but in the  end....  it  will all balance  out  anyway>

I put the  completed  trade  transactions all together  with  my  copy of the  return for  easy tracking... I  also use  quicktax. I like to plan in advance  what  I will be  paying  and    take  flow through  placements to  reduce  tax  exposure...... have to  watch out  for  alternate minimum  tax  though. It can  render  flow  throughs  usless if you  make too  much . 

Not  suggesting   you  do this method....  but I  have  been  doing   this  method for  about  15 years now... and  I'm  not  going to  change now.