put engine back in bike after replacing stator

after repairing the stator and reinstalling the engine now I have three small problems 2 of which may be related
first the neutral light dosent come on and the clutch must be pulled in to start
second the high gear light also dosent come on
third after riding bike i may stop real quick for something it has a really hard time restarting almost like a struggle due to compression especially if trying to start it in gear

Sounds like your neutral and O/D wires are unplugged. Both wires come out on the front of the engine. Since the circuits can't tell you are in neutral, the clutch must be pulled in to start.
Struggling to start when hot - inspect ground and starter cables for internal corrosion. It takes a lot of current to spin the motor when hot.

Yes and check the main ground wire is tightly connected with clean contact surfaces.

what do these plugs look like are they the same wire or is it the round double plug on the top of the engine near the timing belts all plugs and wires seem to be attached

On the left side of the faux tank, it is the black connector with red tape... I think. There are only three wires: Green/Orange, Red/White, and Green/Red

Ive looked at all connectors over there all are connected and some r going into main harness I cant seem to find any with those color wires in it
Just where does the neutral switch and overdrive lite connect on the engine and are they the same wire or wires

ive looked and found the gear shift sensor and a relay and none of the wires connected to it even come close to anything the book even says I never touched any of these wires at least not up there on the rt side of ignition unit only wires we touched were those neccessary to remove the engine

The connector needs to be disconnected in order to remove the motor. It is on the left side of the bike under the faux tank.

This is it on my 84 standard and it's at the same place on my 87 interstate

Brian Thanks for the pic. there were only 2 sets of wires that were disconected to get the motor out , they were crossed from the left side connections down to the right side of the engine , and they are both connected. all wires are connected including the three sensor wires that were on the motor, the lrg round one with 2 nubs, and the single one , both by the gooseneck for radiator. the other is one that has a small screw to connect it
would any of these problems be related to the wiring on the clutch lever I replaced that turn signal and horn and dimmer assembly also (horn button broke)

The gear position sensor is an internal component of the engine. It is bolted to the inside of the front cover and the wires come through the front of the motor, so that plug must be removed to remove the engine. The only thing that would reasonably cause the problem you are describing is either the sensor went bad or it isn't connected.

Check to make sure the wires are plugged into the correct connectors. In the mass of connections and plugs under the shelter, there are unused connections that you may have plugged the three wire connector into.