today I got around to putting the springs and control arms in as well as the front koni struts but I put the supplied washer and bolt on with a set of j&m caster plates and I'm worried the bolt cant get enough thread.

I snapped a few pictures

 

maybe use a thinner washer under the locking nut.

 

you arent using the factory dust boots are you?

 

if the car is still up in the air, put it on the ground partially to push the strut up more and thread it down.

 

Remove the factory dust boots

 

It just has a some after market dust boots, just rest at the top they arnt between the strut mount and the strut.

as for lowering the car to push the strut up further I put the struts on before anything else.

On the opposite side I took the space/washer out and it looks much better, is there any harm in doing this?

 

taking it out completely MAY cause some friction, or so id think.
get a thinner one...as said above

 

What is the right dust boot to use with the Konis?

 

Are you referring to the black cover that goes over the strut (seen in the wheel well) or the dust cover that sits on top of the strut mount (seen with the hood open)

I re-used my stock wheel well dust covers on the Konis. Seemed to fit fine. I don't think you can use covers on top of the aftermarket strut mount setups.