SW20R.
So how did you shorten them? Did you cut along the ridges of the boot itself?

Yes! 
I cut along the inner edge of the fold.
It is quite easy to do if you use a Stanley knife.

I have some new Koni yellows for my SW20 getting shipped to me at the moment, so I'm looking at ordering new OEM strut boots for front and rear and I want to make sure the fitment is ok.
Does anyone know if the Koni shock absorber shaft/rod diameter is the same as the Toyota OEM ones?

I'm not 100% sure, but I just fitted Koni inserts and used KYB bump and boot for the rear (as bump is 45mm) and bought Monroe 63619 for the fronts which I cut the bump down to 35mm. The Monroe boot is more of a rubber(which comes with zip ties), whereas the KYB boot is more of a plastic and will just slip over gland nut. The thing I did note is the thread on the Koni is different to standard, as I couldn't reuse my front camber tops with them.

whitemr2gt - yes, they are the same diameter and fit perfectly. I just replaced my boots (With attached bump stops) with genuine toyota ones and am running Koni yellow struts. Check the parts catalogue, but you may want to replace the foam like washer as well at this point. I found mine was totally disintegrated when I pulled it all apart. Also check the strut tops to see if they need replacement.
 
If its a 92+ MR2, reverse the front strut tops when you re-install to gain extra castor. For memory the little arrow on the strut top faces to the rear of the car for the extra castor.

P E T E
 
If its a 92+ MR2, reverse the front strut tops when you re-install to gain extra castor. For memory the little arrow on the strut top faces to the rear of the car for the extra castor.

It's actually the early model pre '92 strut tops that have offset centers (4 mm) and the the scalloped side normally faces to the rear of the car.
If you reverse them (scalloped side to the front) you will gain an extra 1 degree of caster, and it wont affect front toe adjustment.
By doing this on my '90 model I could get up to 5 degrees caster total with the caster adjustment maxed out,
but IMO makes the steering too heavy for normal driving.

whitemr2gt
I have some new Koni yellows for my SW20 getting shipped to me at the moment, so I'm looking at ordering new OEM strut boots for front and rear and I want to make sure the fitment is ok.
Does anyone know if the Koni shock absorber shaft/rod diameter is the same as the Toyota OEM ones?

As PETE says they are the same diameter, and the stock bumpstops/boots should fit ok.
Konis are good gear, but a few things are different.
You can't reuse the OEM gland nut, and will need to use the supplied gland nuts that come with the Konis.
Check to make sure that the thread is correct; I have seen some that are not.
BTW, the split plastic washer sits on top of the gland nut to stop air being pumped into the top of the shock if the suspension bottoms out on the bumpstop.

Also when you reassemble the struts make sure that the flats at the top of the shock shaft align properly with the corresponding flats in the top spring seat. Very easy to get them misaligned.