99 taurus transmission shifts funny when hot from first to second what could cause this?

The trannys on these cars are notoriously fragile. I would recommend you drop the transmission pan and replace the filter, followed by having the trans flushed, to clean out the torque converter.

I have done this and it still has the same problem. What should it cost to replace the trans?

I paid 2K to have mine rebuilt on my 2001. If you are planning on keeping the car a long time look at Jasper transmissions...they will cost a bit more but are well built from everything I have heard.