Hi Rich,
One of the big things I learnt was (obviously), measure twice, cut once.
This website is the best for a huge amount of knowledge, so take your time and read and seach the threads (I couldn't have done it without the info here.
Do a lot of mock ups and keep re-checking your measurements.
When it comes to boring the KX500 rear mount, take it to a engineering shop with a drill press. Get them to get the dummy alignment with a 15mm drill, bolt the engine down, then go for it with the 17mm. I drilled it with a 17, and used an adjustable hone to take a very small amount out of the bore to make the bolt go in easier.
I was lazy and bought the SH exhaust with a Q series muffler, so my bracket dimensions are not the same as everyone elses. The SH hose kit is very cool, but I did some mods to it to be able to take the existing KLX450 radiators with only one hose outlet modification. Worked a treat and I can still use the aftermarket radiator protectors.
I used the original lower brackets of the KLX450 (same frame as yours, or close enough to it). I didn't grind any of the frame at the rear engine mount, I just used a bottle screw jack and pressed it out about 2mm to get the engine and swingarm in with the bolt. It is a tight fit.
Frame rails from JFAB are very popular, but I ended up making inserts with internal spigots. Personal choice.
Take you time to read everything on the site. It is excellent.
TSF