I reckon the guy who built the model you posted either used an aftermarket canopy, or moulded his own. As Wojtek stated, moulding your own is the eassiest and cheapest - if you know how to do it. I can post a short tutorial on this, but it might not immediately solve the problem, as it takes a bit of practice to get the job perfect. And even then, the first couple of mouldings can be wrong sometimes.
Personally, I'd shy away from trying to heat and re-form the kit canopy - it could craze, deform or break, and obtaining an accurate adjustment would be difficult, especially as the kit part appears to be a bit short in height (or depth of the lower frame).
I think Dwight is on the right track.
It appears that the kit part will fit over the centrre section canopy, but is prevented from doing so fully by the thickness and angle of the bottom of the pilot's canopy.
Here's the way I would go about it.
First, refer to the pics, and identify where the 'glass' should end, in relation to the lowwer frame. Next, tape both sides of the canopy at this line, to protect the clear areas. Then, carefully thin-down the part, on the inside, by shaving with your scalpel blade. Only reduce the thickness slightly, begining on the extreme bottom edge, cutting at a 'V' shaped angle, as if adding a chamfer.
Then carefully sand/file, checking for fit over the 'fixed' canopy regularly.
When you are saitisfied that the sliding part will sit over the fixed part correctly then, on the inside, with the tape still in place, add a thin, short strip of plastic card, the length of the bottom frame, which should protrude just below the bottom edge of the moulding. The real canopy appears to be slightly deeper, and what you are now doing is replicating the panel of the lower frame. Match this strip on the outside, by adding another thin strip, butting aginst the kit moulding, and glued to the inner strip. Any trimming to correct shape and length can be done when the pieces have fully set.
If there is a visible gap or joint-line between the outer strip and the bottom edge of the kit part, this can be filled with PVA, or a mix of varnish and talc. The former can be smoothed out with a wet finger tip, the latter very lightly sanded, if required, when set.
Judging by the size and shape of the kit parts in your pics, I reckon that, short of moulding a new canopy, the above will be the best option, and should look convincing and accurate.
Hope this helps.