Your shift fork set up is correct. Mama Kawa made a mistake and switch the numbers in the manual pic F69.
Take a look at the pic F63 (#52->5th and #58->4th gear) and pic F78 of the 4th/5th gear position on the output shaft.
I finally managed to get the engine components vapour blasted last week. No excuses now for not proceeding with this rebuild. The photo below shows the engine with the cleaned parts in correct position but not actually installed. It's been so long since I disassembled everything that I've forgotten where I put some of the smaller parts. Luckily everything was bagged and tagged, so my only issue is finding the bags. Most are in one bin but a few went into other locations.
Yesterday I put the pistons on and slid the cylinders over. In the past I've always done it in the frame but this time the engine was sitting out of the frame. Much easier! Maybe it's because it's a 650 but I was able to wiggle the cylinders on top of the pistons until they just slid into place. Today I started to put the valves back in. I'm lapping each one as I go and then installing when I have both valves for each cylinder ready.
I have several restored bikes along with a 2006 Goldwing with a sidecar. My wife has a 2019 Suzuki DR 650 for on and off road.