I put one quart in the frame and the other quart 'n a half in the left intake hole. Since most of the assembly is on the right side I put the bolts in from the left and nuts on the right. Your correct on the valve clearances.
Steve in SF
87 Harley FXRS-SP ~ 06 KTM 625 SMC ~ 72 Honda CB750/915cc ~ 92 XR600/654cc ~ 95 XR650l/675cc ~ 03 CRF450r ~ 05 CRF450x ~ 02 XR650l/675cc ~ 86 YZ490 ~ 93 YZ80 ~ 93 XR650l Project