If you're getting good spark then much of the electrical system is ok. That's very good news. The bike should run now, although there may be another issue keeping it from starting such as gummed up carbs, bad gas, clogged air filter, etc.
Since there are doubts about the regulator/rectifier, you can unplug it for testing. Obviously the charging system will not work but there will be one less variable to cause confusion while troubleshooting. You can always address it when everything else is working.
Are you certain the main fuse is installed correctly and is the proper value? With the battery hooked up backwards it should have blown quickly before any wiring was damaged.
The metal chain securing the battery sounds like an accident waiting to happen. Is the stock battery tray hardware missing? At the very least an insulating material should be used if there is any possibility of contacting one of the battery terminals - plastic cable ties, rope, whatever.
Any time a wire smokes there is a good possibility it has been damaged internally - the conductor may have fused open. This could result in an intermittent connection that could make or break under vibration. My preference would be to replace it.
If a wire has smoked or melted inside a wiring harness it's possible/probable that adjacent wires have had their insulation compromised. This can cause shorts, either hard or intermittent, that can be extremely hard to track down. The short could be buried deep inside the harness with no visible damage from the outside. In this case it may be best to find a replacement harness from ebay or a parts bike.
At this point, it would be advisable to clean up any wiring that appears questionable. Keep the regulator/rectifier completely unplugged. Try to get the bike running - since you have good spark, concentrate on non-electrical problems.
Finally, return to the charging system when it's running. If the wires are smoked on the regulator/rectifier my preference would be to replace it with a used one from ebay. Even after thirty years the Honda units are extremely reliable and I would not hesitate to install a used one.
You'll need a multimeter to properly assess and troubleshoot the charging system. See this writeup.