When modifying an atv frame for any purpose it is essential that the frames integrity is maintained.
Alot of frames develop cracks in them in the same places, these are normally repaired by adding some reinforcement to that area.
When doing some serious modifications to a frame such as changing the type of motor that's in it then you will need to be sure that whatever work is done it will meet or exceed the factory strength and integrity.
The first thing to do when installing a different engine in a quad frames to align the counter shaft sprocket with the pivot bolt for the swingarm, this will keep the chain from getting too loose or too tight when the rear shock is compressed.
After the countershaft sprocket is aligned then the next thing to do is to align both the front and rear sprockets with a chain, you will need to move the motor side to side and twist it to get it perfect ( be sure not to change the up and down of the engine or the pivot will be off)
once everything is aligned just right then this is where the motor needs to be mounted, depending on the type and size of motor and the frame that your working with you may need to cut out part of the stock frame, if this is necessary then you will need take extra special care that the frame is rebuilt with the same or greater integrity as the OEM set up.
If you are installing a large engine such as a street bike then you will most likely need to cut out and rebuild the entire upper and lower sections of the frame.
This is a little more difficult to do because you will need to keep the same alignment of the front and rear frame sections while building the new center sections, the best way to do this is to tack weld the front and rear sections to a steel work table or homemade jig to hold them in place while you cut out and remake the new pieces.
when welding in the new frame sections you will need to be sure that the old frame and the new frame pieces are sleeved or gusseted or the will break really easy, a sleeve is best if you cut at least 3" - 4" of tube that will fit inside the factory and the new pieces tightly, once it is fit into both pieces evenly then you can weld the seam, make sure that your weld penetrates deep enough to attach itself to the inner tube, then drill a 3/16" hole about a 1/2" away from both sides of the weld and then plug weld them shut, this will connect both the inner and outer tubes together.
Once you have the new frame sections in place you can remove it from the jig.
Usually thereare many other problems that arrise when installing a non-standard motor into a frame, they will need to be worked out individually, just remember that the stress that these frames are under are extreme, make sure to build them strong enough to withstand it all.
Just remember that most anything is possible when you put your mind to it, get creative and build something unusual and cool.
And have fun with it.....