I have done it successfully in the past, but make sure the jumper is indeed removed. Also ensure you use as much 5V and GND wing pins as possible to lower noise and increase current capability.
However, I wonder if you are replacing a PROM which used 5V as IO voltage. In this case DO NOT connect it to the wings, since IOs on the FPGA are 3.3V. There are a few solutions to convert those signals, but will depend on the IO standard (TTL or CMOS) that your system uses. If it's a TTL system, then using some 5V-tolerant buffers should do the trick.
I have a design which interfaces a 3.3V FPGA to a 5V TTL system, and seems to be working OK, I can send you a link for the project if you are interested.