One option that you have is to buy a tail light / indicator combination like this:
http://cgi.ebay.co.uk/LED-rear-light...item563872f498
It looks brilliant, neat and tidy!
Another thought I have had, is if you have cut your tail down you could have them sticking out left and right from the bottom of your numberplate, that way they would not foul the exhausts. .!!!!. (.=indicator, !!!!=numberplate)