I see the problem with the McLaren. It's not something I can tell you how to fix without having a proper look at the 3do, but here's an idea that popped into my mind:
I think the wing plus support struts are one single 3do file. I would split them into three, one for the wing, one for the left strut and one for the right. Then I would rearrange the 3do tree a little bit so the left strut is situated in the left part of the engine block 3do tree and most importantly has the right plane node (that is why your wing strut is clipping), and the right strut on the right part. I would probably leave the wing at the same location in the 3do tree.
I would take a look at a car with similar wing struts to see how they solved this problem, and maybe nick the plane node from to implement with 3domerge so you don't have to create one yourself (I'm a lazy person

). Maybe taking a look at the '69 Brabhams high front wing would suffice, as I don't remember the struts clipping with the bodywork.
I mainly use GPL Editor to look at and edit the 3do's, as Charles Mark told me when I was starting out, it's a buggy program but if you know how to avoid it's quirks it's an amazing tool and the sky is (almost) the limit for editing GPL cars

. I go to the PRIM (primitives, where everything how GPL reads the car is stored) and click on a node (branching point of a tree) and hit F2 to see it. Sometimes the tree is too deep or confusing for GPL Editor to draw, so it can be tricky to find stuff, but luckily there's the node repository so you just look around there clicking nodes and hitting F2 untill you find something you look for (or close to, say you're looking for an engine and you find a rollbar or exhaust header) and then hit F3 to fill in it's offset to have GPL Editor find that node for you in the tree.
If you know what to do this job takes between half an hour and an hour, but if you are just starting out it will probably take at least ten times that because the amount of information given to you by GPL Editor is quite overwhelming at first and you need to first figure out what you need and what you don't. A thing to remember with GPL 3do's is that the planes are at least as important as the polygons, as GPL is not 3d in the true sense of the word and needs some help sometimes to figure out in what order to draw something. So when I merge stuff from one car to another I always try not to forget to include the plane nodes (usually just one branch up from the polygons themselves) .
I'll put a thread up at the GPL Repository soon to show how I do stuff, and I'll attach the programs. Paul Skingley and Charles Mark were very helpfull in giving me advice a couple of years ago and providing me with the programs I needed, and thankfully I had a tiny bit of brain so I saved all our conversations, as I had forgotten everything when I returned to editing this past June

.
Especially in the beginning it will be tricky, for instance when I tried merging the coolant pipe of the Brabham to the 3do file, I got CTD's in GPL. Turns out the cleaning program I used to remove unused polygons and other stuff from the 3do messed up the brabham 3do somehow, literally the last step in the editing proces but it took me a day to find that out

. It's stuff like this you've got to be prepared for, constantly keeping track of what you've done and making sure you've made no mistakes in the process, before moving on. It's frustrating at first but very rewarding later on, much like driving GPL really hahaha.