If they did install them backwards and I have seen a lot of shonky box builds, then the gears will be stuffed, if thats the case I suggest you to just get a second hand box
When you had your car converted to manual, they they throw a strengthening plates between the clutch master, firewall and clutch pedal??
It could even be due to incorrect clutch adjustment
Get someone to press on the clutch while u lay under the car and see how much movement is in the clutch fork, maybe your not getting enough to push the pressure plate in
A common mod when the box is out is to throw a 3mm washer/shim under the clutch fork pivot ball, that will give the fork more throw
Here is how to adjust the clutch
[youtube]http://www.youtube.com/watch?v=vYJxQyjIhUw[/youtube]