You said the bike was running well before the work.

Were you running on the jumper cables while it was running well?

@ Digger, yes since I have been working on it I have been using the jumper cables on the battery wires.

@ Boofer, I did screw/ground the negative battery cable to the frame with the negative jumper cable to the spot where the clutch cable would normally attach to the engine. the positive jumper cable stright to the positive battery wire. I have touched the positive jumper cable directly to the starter but did not check the spark plug while doing this, it did not start though. But I can check it tomorrow.

Another question I  removed the coil from the bike and when I turned on the key the coil magnatized and stuck to the frame, is this normal? Also I get contanuity to ground (frame) from both wire connectors on the coil, is this normal?  Everything looks normal and no "plastic" smell from cdi.
Thanks guys

This bike does not use a CDI. It uses a Transistor Controlled Ignition, which replaces the points of a conventional system. Power is supplied to the coil primary winding from the battery through the ignition switch and wiring. The other side of the coil primary goes to the TCI, the switching transistor of which grounds it. Thus, current flows through the coil primary. When the stator sends a pulse to the TCI, the TCI briefly turns off the current through the coil, in just exactly the same way that a set of breaker points does when they open. The abrupt stopping of the current causes the coil to produce a high voltage in its secondary winding, which is led to the spark plug causing it to spark.

I suspect the TCI would not cause a weak spark. It would probably fail completely instead. I rather doubt problems with the coil, too. I don't have the numbers handy but there are ohm checks for it. Since the original post says the engine was removed and replaced, I'd be looking at all the wiring involved with that, especially including any connectors that might be incorrectly seated. Savage 87 already suggested you actually install a good, fully charged battery instead of using jumper cables. Remember the starter pulls a good bit of current - some tens of amps - and the jumper cables will cause some voltage drop. I think your "weak spark" problem is just low system voltage during cranking.