A quality video of the rattle/knock with sound can speak 10,000 words.

Based on what you've said I reckon you've spun a  big end bearing. I had the same thing happen to an MR2 I had years ago. Huge knocking sound while driving. Car still drove till it ripped up the crack bad enough that it just ceased. Best to tow it to a mechanic as every time you start it, would be doing more damage.
Cost me 2k for a bottom end rebuild.

I spoke to Ian, and he said possibilities is bottom end but can't guess and actually have to open the block to see what's been done to it by previous owner weather it's worth fixing or replacement motor, so yesterday was first day started working on it, if i have a decent motor il probably rebuild it depending on the extent of damage,,,

Providing the crank can be ground down you would be better off rebuilding the bottom end, I have seen people throw used engines in with on ~ 80,000kms and last a few months, unless you have x-ray vision there is no guaranteed way of telling how good a second hand motor is.
 
Atleast if you rebuild it you know the bottom end will never pop again, providing the machinist gets the clearances spot on.

Finally the engine is ripped apart and by looks so far definitely bottom end and engine has been opened up before most Likely by some one that loved blue silicon, but now the decision of standard build or forge and go all out?,

might as well go the best you can afford while the engine is out and already opened up.
forged pistons and stuff arent that much more expensive compared to OEM stuff.
gorilla industries have a real good deal on engine rebuild kits have a look in there
cheers 

Well depending on your budget and current modifications I would recommend getting forged pistons and H beam conrods.
 
A set of Wiseco Forgies and Eagle H-beams can be brought for around $850 and a set of ACL race series rod + crank bearings are around $150, and there for less than 1G in parts a fordged bottom end that will hold up boost, also I would highly suggest getting a MLS head gasket.
 
What mods do you currently have now? are you planning on running higher boost or upgrading your turbo?

If you had spun a bearing you'll see metal shavings when you drop the oil now. Additionally, may help or not but good to know. HKS cams are somewhat "soft". Mine have a few flatspots (been running them for near 10yrs) which makes my cylinder head kinda "noisy". Valve clearances etc are all perfect too.
 
Either way, a decent mechanic (probably not the one you just went to) could identify/diagnose the issue. Does sound like a bearing though.

MR2QIK, did your HKS cams make a bit of head noise from the flatspots?

I decided to get a engine n rebuild my old one as a project,
With a bigger head ache the car is still not running thanks to two work shops that not only f****d me nicely but left a nice big hole in my wallet too,
So now,
After everything and car catching on fire it still continued to mis,
haveing to work on it my self I had a vac leak from plenum decided to replace it n get rid of tvis replacing it with a plate (not sure if it was a good idea)
started car drove like **** kept missing and I just can't figure out why,
put it together again and now my alternator ****s it self
Better yet I got EPA for exhaust noise, aswell
So now I'm sick of takeing short cuts
I have to do it once or it's gonna be up for sale,
I removed my piggy back so running standard computer, in my wireing loom I've got a lot of different plugs not connected and I can't find where they go.
My biggest questions are,
Is there any diagrams for complete wireing plugs for the engine bay? What plug goes where so I can get rid of the rest,
Would the standard ecu be affected by Removeing tvis,
A diagram of vaccum hoses?
What are the biggest problems with the gen 2 motor ecu,
And is there any prossibilities of why it's still missing and still haveing a vaccum leak,

I have never come across a car with so many problems and so many dumb mechanics

I just wanna sit in the car and drive it and go to a mr2 meet lollll

If anyone can help me ill buy u u a slab dead set,