I have a bad a** knocking sound in the gear box, i think i've worn it out pretty good. Taking off it shudders and slowing down off the throttle it shudders, checked engin mounts and clutch, noise is coming from gear box. Is it worth reconditioning or should i just get second hand?

If you're going to keep your car for a while, then a reco box is worthwhile. The downside to that is the cost. But if you're planning to sell it soon, then go for a secondhand box. If you buy it from the wreckers, you can probably get a 1 month warranty on it. From eBay or private sales, you take your chances.

Before getting another box, I'd suggest letting a competent mechanic to assess it. Might be something easily fixed.