From looking at your photos your issue is not whether or not the Mid pipe is an H pipe or an X pipe. Either should fit just fine if designed correctly and routed properly.
The stock H pipe is a 2.5" pipe although many report the actual diameter is less and closer to a 2 1/4" setup. Your issue is that you have a 3" mid pipe that appears to not fit properly due to the overall diameter and the actual routing of the pipes. This can be because of the X pipe itself or because of your stock style headers.
If for some reason you believe an H pipe will fit better than an X pipe here you go:
https://lmr.com/item/SVE-5250B/1986-...ff-Road-H-Pipe
or this one:
https://lmr.com/item/BBK-1507/86-93-...Shorty-Headers
Although I believe you will find that the H or X doesn't matter as that should be located behind the transmission mount and well out of the way of your current issue.
IMHO your issue is the same that many of us face when modifying these cars. You have a plethora or parts that may not have been designed to work with one another and installed in a car that never had dual exhaust. Once again when possible a system approach is often the best option because the parts are designed to work together and should with little or no modifications. I am just as guilty of mixing and matching parts as the next guy as budget, time constraints, etc. will do that. Heck my PC has a 91 5.0 with 95 aftermarket shortie headers and a BBK 87-93 midpipe on it with OEM 03/04 Cobra IRS exhaust. Does it all bolt up, clear, and work . . YES! Did it require tweaking and modifications . . . YES!!! When I redo the car, it will get a different/better setup, but that was what I had available at the time and it fit the budget.
IMHO the exhaust shop didn't want to mess with your setup and just told you it wouldn't work. I wouldn't use them again. As stated above your engine isn't anything super powerful, plus the stock restrictive headers don't help, so I would install the OEM H pipe and run it as is for now.
The issue you are going to have with your Magnaflows is that being 3" they are not going to fit any NON 3" H pipe without having to step up and step down the tubing if using a more standard 2.5" unit. When you make enough power to need the flow of a 3" cat then you will definitely want a 3" mid pipe and most likely will need/want long tube headers. Until that point, a 2.5" system will work just fine and not cause you any issues. Good luck!
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