While this advice about tightening the axle nuts with the bike upright is generally sound when the bike is in working order and without issue, that is not the case here. I wanted the OP to flip their bike over for diagnostic purposes. This eliminates the force of gravity pulling the frame and fork down onto the axle and gives a better idea as to whether the fork dropouts are in alignment without using the weight of the bike to force everything to fit. Pushing down on the bike to seat the axle into the dropouts is good advice when you are sure the fork isn't the problem. But until you can rule the fork out as a cause, don't assume the dropouts are in alignment.

As for a bike needing to be upright for repairs, that is not true. Countless people without the benefit of a repair stand adjust brakes, true wheels, repair flats and numerous other tasks including washing the bike itself while it is upside down. In fact, i would even recommend washing it upside down if your bb she'll doesn't have small drainage hole. Without the convenience of a repair stand or similar construct, flipping the bike over is fine for many repairs. Notable exception is the fine tuning of the shifting of the front or rear derailleur. The chain will not 'drop' onto smaller cogs properly or on a manner consistent with the way you will be riding when the bike is inverted. And working on a hydraulic suspension fork with the bike upside down is highly discouraged.