I dont think rubber washers will help I used grade 8 bolts and steel lock nuts with grade 8 washers where ever I could get them to fit.
Probably overkill but I dont have to worry about the bolts shearing off, I do worry about the engine breaking in half though.
I suggest starting with the big engine mount bolts, the top rear and bottom rear but if you got the long top rear bolt just do the bottom rear and then the four at the front.
I feel the three at the top near carb are least important and easiest to do but you have to remake the top three hole brackets(simple to make)
The big rear bolts and the front four bolts do more to firm up the bike frame overall and the two rear bolts in my opinion are best to get set first since they will help keep the chain properly aligned with the engine.
On my bike I changed all engine bolts and had to remove the brackets for the long useless, stupid, wimpy top engine bolt and welded in some brackets that allow me to use the same length bolt there as is on the bottom.
On my wifes bike I just left the long bolt and changed the rest and it has been fine but I will be changing hers around like mine soon.
The engine mount bolts are one of the most dangerous and damaging things I have seen on these bikes and lead to all kinds of trouble.
(vibration, chain/sprocket damage, possible engine damage from thrown chain, possible bodily injury caused by rear tire locking up causing crash from thrown chain,possible frame failure since engine completes frame)