FFmpeg MP4 to FLV too slow
Given your are using a VPS this is no suprise (guessing you only have a single core with 1-3GHz) and you won't be able to crunch the conversion down to a few minutes. You can try using -c:v libx264 -presets ultrafast but I'd guess it will still take you about 45-60 minutes to encode.

Also remove the -crf option when using a preset (they choose a default that produces a very good balance between speed and quality, I only recommend to modify that value when you know what it really does)

Be advised that the quality you get from that preset is not exactly great. If you NEED fast encoding speed over everything then go for it, if it's not THAT important I'd suggest using fast oder faster instead of the ultrafast preset.