Hi! Welcome to the forum! And welcome to the love of Fieros!!
As far as which cars to get, do you have any preference of fastback over notchback or visa versa? Since both GTs are fastbacks, if you prefer that style, it would be a great choice. Conversely if you like the notchback better definitely get the 86 SE. Another thought is, do you have any preference for manual or automatic? And of course if one car is going to be for your grandson his preference may matter too, but as a 4 year old, if you tell him your preference he will probably agree.
Another factor to consider is the options they have. Power doors/ windows/mirrors, which stereo, trunk release, rear defogger, etc. One of my Fieros came with no options and I took several years to find and install all the options I wanted which could have been spent on other mods if the car came fully loaded. Since the ones you are considering are GTs and an SE, they probably have similar options, but still something to consider.
Interior color is another thing to think about. If the cars have different colors which do you like better. There are many great vendors like MrMikes for seats, Russ88ttops for upholstery and others that can help restore the interior if condition is poor, but changing color is another level of work to do.
Since you are experienced with cars and have goals to do a lot of mods, engine swaps, etc, mileage probably isn't a big issue to worry about. So I would recommend just going off of preferences.
If I was given the choice, I would take the 87 GT for sure and swap the 3800 in it. if the clutch needs replacing might as well just take the engine out and swap in the 3800 while at it.
For the other its pretty much a toss up for me. I actually prefer notchbacks, but I already have 3, so I'd be fine with taking 2 GTs. It would come down to the color and options on those. Or the low mileage could be nice on the SE, I've never had a Fiero with under 50K, so that might get my choice.