Make sure to check the HT leads and spark plug caps too when looking at the coils. The rear ones will be easy to get to (just take off the seat) but the front ones are a complete PITA to get at - totally buried.
Often the ends of the HT leads get corroded, and when hot it can lead to a weal spark. Also the spark plug caps can crack and get a bit **** when hot, and then they arc and you lose spark. To fix the HT leads corrosion unscrew from cap, cut 1/4" off then rescrew. See if it helps..
If you have any issues such as cracked coils (very common), ***** HT leads or plug caps, the best thing to do is dump the lot and do the Coils Over Plugs mod. Ask 88vmx12 for a complete kit (supereasy top quality plug&play), or get the bits off fleabay and DIY.
Another possibility is that your TCI box is playing up when hot. The only way to find out is to replace it with one known to work to see if it helps. Ask Sean Morley to hook you up with a loaner to try..