When my Honda is in neutral it reads on the dash that it's in 3 could this be the shift angle sensor ? I'm lost on this

 

No, On standard ES models there is a rotary switch in the alternator case which connects a wire up for each gear in turn, this info goes into the digital readout and comes up as the gear number. However the ECU controlled setup on the auto is so complex I'm not sure the same system is employed. All the angle sensor does is tell the electronics that the shift motor has turned the mechanism far enough to change a gear.

 

I have to hold the break to crank and when I go to shift to first it's hard for it to but reads 4th gear how do I fix this

 

As I wrote above seems like the gear position switch reading wrongly. Have you had the alternator case off and put the switch back 180 degrees out? On swinging arm models the whole arm assembly has to come off to remove the alternator cover, I expect a similar method will be requires with the IRS rear end. There is a grey plug and socket usually under the rear plastic, behind your right thigh when you are sat on the bike, this contains the wires from the switch, I guess you could test the wires to check if it is a faulty switch. You would be best getting the workshop manual, which will show what colour wire is for which gear, and how to remove that alternator case, if needed.

 

Yes i have had the case off changing out the balancer gear and when I put the motor back together Is when I notice it was reading the wrong gear is it the shift angle sensor you are talking about

 

Wow, never heard of a balancer gear giving problems, but you have put the switch in 180 out "been there done that" on a 350 years ago. The gear position switch has a roll pin through the shaft which engages in a slot in the end of the shift drum, it is slightly off centre, as is the slot, same idea as a lot of old fashioned car distributors used to be, so in theory you shouldn't get it wrong, but the offset is so slight it is quite easy to put it in 180 out.I repeat,no it isn't the angle sensor, it is inside the alternator case.