How many of you have ever stuck the 652cc thumper in a completely custom frame and made a new bike out of it? I am strongly considering this just because the frame of a savage doesnt work well with my height... and id rather use a complete new custom frame than have the stock one chopped up and extended and etc. Also if you have done it or your an experienced fabricator and such, what would you do about the engine mounds and aligning the sprocket (obviously chain conversion) to the rear wheel

Kinda rare, like size 18cheerleader outfits.

Having done it I would ask you what exactly are you going for in your transplant?  I did size up many Suzuki frames as that is my back ground.  I ended up with a 1968 (Montgomery) Wards Riverside Mojave frame that was actually made by Benelli in Italy and was a knock off of a Rickman Racing frame.  

There are a couple of companies that offer frames for the LS650 engine but they are rare.

I am about to transplant a 1970 T500 2 stroke into a 1970 Colin Lyster racing frame.

It all can be done.  The question from me is why?  What is it you want to accomplish.  The stock frame does have some limitations but are they real world limitations?  not so much.  I have been amazed at what people have been able to easily accomplish with the stock frame.  That said I would have to say it is a pretty good base to use for a project.

Tell us more what you are going for.  Look? Size? or Geometry?etc.