The first thing this brings to mind is the fact that most Acer, HP, Compaq, Dell and other OEM style systems often use proprietary motherboards that don't conform to standard form factors. There might have been differences in where the standoffs were located.
Now that you have a non-OEM case and motherboard though, that shouldn't be a problem. What MIGHT be, is if you do have a standoff installed in the motherboard section of the tray that doesn't conform to exactly where the standoff holes are in your micro-ATX motherboard. I would double check that there are no standoffs under the motherboard that do not directly line up with a standoff hole IN the motherboard. That will mean removing the motherboard to check. If you are 100% certain that is not the case, then cool, it's one thing less to have to consider.
Being as you have a 7th gen CPU but only a sixth gen motherboard, you will NEED to update the bios to a version that supports the 7th gen processors unless you KNOW for certain that yours has already been updated to at least whichever version added 7th gen support. 7th gen processors won't run in a 100 series motherboard without a bios version that is new enough to support it.
Updating to the latest bios would be even better, but you will need a compatible CPU in order to update. That means you're going to need to borrow a Skylake 6th gen CPU from somebody OR buy the cheapest one you can find that will work in that board without an update.
New, that would be this:
PCPartPicker part list /
Price breakdown by merchant
CPU: Intel - Celeron G3900 2.8 GHz Dual-Core Processor ($41.25 @ B&H)
Total: $41.25
Prices include shipping, taxes, and discounts when available
Generated by PCPartPicker 2018-12-28 02:49 EST-0500
Although you MIGHT be able to find a used one cheaper. That's kind of a crapshoot though as you don't really have any way of verifying that a used CPU is good before purchasing it. You can minimize the chances of getting a bad CPU by buying from a seller on Ebay with a good rep and a lot of sales though.
One thing that kind of bugs me is the fact that you say it was an "old" acer motherboard. Was that i5-7600 installed in that "old" motherboard or is that new as well? I'm not sure that I'd consider Kaby lake to be "old", but technically it IS two generations back so I guess so. LOL.