I resently bought a 48" farm jack (hi-lift clone). The base plate isn't ridgid to the jacks main rail, it woobles around , is this normal? How do you position the jack when lifting the car?

That is normal. These things are fairly loose and rattle. I am not sure why, but it may be it is less likely to tip over if it has some flex? I reccomend using a plastic high lift stand. As far as positioning its a matter of having it very straight up and down, on a flat jack point and many times balanced.(example, if you want to jack both rear wheels at once, or work on a spring and go very high, the jack will have to be DEAD center or the truck will slide over. All this assumes aftermarket rock crawling/ wheeling style bumpers as its priety useless with stock bumpers. Remember safety too, these things are very shakey, and the handle can fly back up when letting the vehicle down.

Yea, especially with the cheaper versions of the Hi-Lift. Also, those will waer out and quit working much, much sooner than a real Hi-Lift. I know, I tried to go the cheap route at first too. Then realized I would be buying 3 or 4 of those instead of just 1 Hi-Lift.
Of course, if you only use a few times a year, then it might last a few years.
The stock bumpers will hold the truck, but you will bent the bottom lip of the bumper most likely.

I always jack my stock bumper directly under where it bolts to the frame. No bending, however it does pust the back of the bumper up a bit. Just get on the bumper when done and jump on it a couple of times and it will go back down. For the front, I have a custom bumper. I can jack pretty much where I want on that.