Thanks for the replies above.
Well i have finally got everything sorted. I also had problems with my visa but to my surprise, the american embassy were very efficient in sorting it out.
I emailed the tsa and explained my problem. They responded almost immediately. I was told that i could submit my application without the passport by indicating that i would fax it. When i did this i recievd the fingerprint instructions in about one day as well as instructions on how to pay.Ive since emaled them a copy of my passport so now the next step is to get fingerprinted in the U.S.
Overall both the embassy and the TSA were extremely efficient in processing my applications. If i had done everything correctly from the start im sure i could have got the visa and clearance from the tsa in one week!!
For anyone else going throught the process i would suggest giving yourself a lot more time to reduce the stress involved.