In the later cars at least, the trans tunnel opening for the manual shifter was longer than that of the automatic. But the required "cut out" was well defined in the sheet metal. I've done a couple of these. They also have a boot that bolts to the top of the tunnel with a metal flange to hold it in place - unlike the early 240's that had the boot that just slid over the sheet metal and was supposed to hold itself in place... I haven't seen an early replacement boot that actually fits well or stays in place without adhesive.

You have the boot out (or can take it out). Did they modify the hole? You can probably tell if they cut or ground the edges of the stock opening. The stock opening will be completely covered with stock paint and no bare edges...

 

Yes the later auto zs had a glued in bolt pattern smaller than a manual. However there were no us 5sp 240s so there might be a significant difference.

 

It would appear the hole has been enlarged. I think I found a boot for a Jeep that will cover it.

The conversion was done almost 25 years ago and I just asked for a 5 speed, if they told me what year car the transmission was from I have long since forgotten. It does look to have the shifter further forward than where it should be?

 

Yup, it's been cut forward. You can see the original opening in the sheet metal... Also looks like this would have been a "monkey shifter" car - the series one transmission - if it had been a manual transmission car.

With the modification you'll definitely need to find a non-stock boot to cover that.

To the point above, The 2nd generation 4-speeds and the 5-speeds had the same shifter configuration - they were essentially the same transmission with an overdrive gear added.