Found the solution so I'll answer my own OP
The answer for anyone else wondering about this is - AVS Video Editor
The MKVs import straight in without issue and it looks pretty feature packed for video editing to a wide range of formats with some nice advanced options. You can buy a 1 year access subscription for $39 (US$ I think) or an unlimited access subscription for $59 which from the looks of it, gives you access to download and fully utilise any of their range of products for video, audio, image converters, editors, players, etc plus other misc apps (around 16 different apps I think). You can also just download the trial of AVS Video Editor and still get full feature access to the application, you simply have to put up with a watermark that goes away after 1 minute into the video you produce with it.
http://www.avs4you.com/index.aspx
Hope that helps anyone in the same predicament I was in...I mean that guide for converting to 60 FPS is great but the MKV files it leaves you with are almost useless for editing afterwards unless you have the exact right software.
Cheers,
Craig