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I know you can strafe with ctrl+left/right but I prefer the WASD method and I have that setup now. I can't seem to have Q/E setup for strafe though. Is there a way to bind both left/right and ctrl to one key at the same time?

You *might* be able to do this with DOSBox Keymapper (Ctrl+F1 to enter), but I haven't used it. Google it to get some help.

If not, there are some programs which do this.

(I haven't used any of the programs mentioned myself, so can't help you there).