How to debug in taint mode (cgi-script)?

After reading through this newgroup I am convinced I need to turn on
taint mode in my scripts. The problem is most of my scripts do nut run
with taint mode on! I either get "Internal Server Error messages" or if
i run from command line, I get "Too late for taint mode option". Any
ideas besides brute force breaking down my scrips to smaller manageable
chunks.