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Do you guys have any suggestions on how to clean the engine before I start my top end rebuild?

Thank you.

Purple Power degreaser has always worked well for me along with a tooth brush. If the motor is already pulled out of the bike you can plug and tape off all the holes so no water gets inside the motor. Carb cleaner spray also works good along with a tooth brush but can get expensive if you need a few cans or more. With the carb cleaner spray you don't need water to rinse off like you do with degreaser.

X2 on that. I was going to say Brakleen, but they are close enough. I used the little brass bristled toothbrushes on mine along with some scotchbrite pads. I also found some tiny scotchbrite wheels for my Dremel tool at Lowes. I used them at a high speed with the Dremel and they really shined up the metal!

If you are trying to shine it up, you can also get some etching aluminum wheel cleaner to use after you degrease. You spray it on, let it sit for 5 or 10 mins, then hose off. The more powerful ones will pit the aluminum if you leave it on too long without hosing off.