I have a 86-89 R..LOL
Currently a ATC bottom end in it and various years of other
parts.
86's have the short rod. 99% of motor builders use the long rod. I use the short rod. I will switch to the long rod on the next crank because the short rod cranks are like 600 bucks compared to 250 for the long rod crank (prices are approx and I haven't checked in a cpl years).
In 87 they improved the cylinder and again in 88 (bridged intake side). Everyone uses a 88/89 cylinder.
The swingarms are different. Some have a motor mount in the swingarm, later ones don't. The ones that don't are prefered but really not a big deal. The length of swingarm was longer in 86 than 88/89's. I like the longer.
There are electric differences between the years. A 86 CDI won't plug into a 89 (for example).