Ht1kid...  the main reason I mention checking the gap is the manual mentions it.  And many people used to battery ignition systems like cars and some 125's had and maybe they remember that point gap was critical on those systems?  So then after they set timing they adjust the gap and screw up all the hard work they just did setting the timing.  (I know.  I made this mistake myself many years ago) 

DEET once said on here if gap is not "within range" after setting timing, you can't do anything about it because the cam determines the lift..  That's true if the geometry of the points installed is "factory".  If the rubbing block somehow contacts the cam "late", the points won't open as far. 

I've had it happen maybe twice where someone had some unknown points...  probably aftermarket crap...  or something off another bike that somehow fit... installed and the point gap is not within range.  Maybe rubbing block was just worn way down.  New quality points (I prefer Yamaha OEM or Daiichi) solved it.  Max point gap was always too small.  If I ever run across one again I will try to figure out why.  Very rare and never happens with new quality parts or very often at all. 

MarkT I agree 100% especially if aftermarket points are used one time ordered points for my Ht1 when they came in the box It was labeled to fit Ht1,Ct70 and others I tried them and I  could never get it to run right. Yes on cars, gap, dwell and timing 

My first thought is "always" the crank key & symptoms are exactly 'that'. Or i haven't read the story fully.

Talking timing, not sure now what bike we're talking but if it has points & a non adjustable stator plate, all you can do is set the piston at [recommended btdc] & have the point starting to separate at 'that' point. They should be within spec for max gap but can't do much if they're not except replace with genuine i guess. Or don't look at max gap & if it runs at least you know the timing is safe.

It’s my Yamaha CT3 with no stator plate slots. I have a TDC gauge coming this week I’ll keep you posted on the build, thanks!

So I got the TDC gauge in and I’m trying to set the timing the correct way. I’m using the continuity feature on my multimeter with alligator clips. One on the points wire and one clipped on the case and at 2mm btdc I can’t get it to open even with the breaker contact wide open it still rings. Is it possible that something is shorted out?

"Continuity meter" won't work. 

Best tool ever is an aircraft magneto timing tester that senses change of inductance when points open.

OR you can use an ohmmeter with an Rx1 scale <=== Rx1 scale is critical and most "digital meters" bounce all over the place and hard to get a clean reading.  I prefer analog (swinging needle) meter.  Zero ohms with points closed and 1 to 2 ohms with points open. 

That little change in resistance will not be noticed by most "continuity meters"...  they will just beep.  Although there is a version (aka "buzz box") specifically designed for points magneto timing that will change tone when points open....  or you can get a test light bulb to dim...  dozens of ways probably but "continuity meter" would need wires removed from points and then replaced after which probably requires flywheel removal and isn't that easy so not a good method at all.

Jeez...  it feels like I've typed the above 5,000 times.      Points magnetos are not the same as battery ignitions and I guess most people don't understand that. 

i.kym-cdn.com/photos/images/newsfeed/001/855/914/ca4.jpg

That link to photo is kinda NSFW... 

Anyway, it's okay not to know.  Everyone has to learn somehow.  Manuals are a good source and there are "how to" articles and many posts here.

And keep asking questions. 

You'll  be an expert in no time at all. 

 

FWIW I was always taught, check that points gap with them at maximum openiing, and the double check, then check the timing.

Plugs can often cause problems like this - dont ask how I know.

I once had another bike that used to backfire like a shotgun sometimes, I traced that to a faulty choke mechanism, it was not closing off.

Anyway just my thoughts.