Can I assume you have two 25 cent coin mechs on your machines? If there is a dollar bill acceptor I am not sure how that factors in but I would imagine the bill acceptor just generates a set amount of "units" which is Stern's terminology which we can think of as pennies.

Check you Coin Door Settings
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Ensure your machine is setup to payout 25 units per pulse, so that each coin is worth 25 cents. This may be default.

My machine is setup for Canada where we use $1 and $2 coins mostly for pinball. As such my Coin Door was set to register 100 units per pulse, ie 100 pennies per $1 coin. And the $2 coin slot is set to register 2 pulses per coin, ie 200 pennies per $2 coin. Long story short the Units per Pulse is the smallest denomination you can adjust your prices to.

Setup Custom Pricing
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This is not intuitive at all. I found this portion of the Spiderman manual online and the principles are the same.
https://www.yumpu.com/en/document/read/7445122/download-stern-pinball

Clear any preset custom pricing which should bring you back to Custom Pricing with 0 Credits At: $0.25

First and foremost, do not adjust the credits yet, first set your price to $1.50.
* Select NEXT until "At:" is flashing
* Select EDIT
* press + until you raise the price to $1.50
* Select to lock this in
* Select BACK until "Credits" is flashing
* Select EDIT
* + once to set 1 Credit At: $1.50
* Select to lock this in

Repeat the steps above for $3.00 and $4.50

Now lets set the $5 for 5 games
* Select NEXT until "At:" is flashing
* Select EDIT
* press + until you raise the price to $5.00
* Select to lock this in
* Select BACK until "Credits" is flashing
* Select EDIT
* + 2 times to set 2 Credits At: $5.00
* Select to lock this in

You should now have 1/1.50 2/3.00 3/4.50 5/5.00

Now I would certainly test this as I am just fooling around with the settings but everything looks right. I performed the above on a Deadpool Pro which is a Spike 2 machine. I did a couple of test simulating a $1 coin as 25 cents and this seems to be working.

The TL;DR version:
* set 1 credit at: 1.50
* set 1 credit at: 3.00
* set 1 credit at: 4.50
* set 2 credits at: 5.00

You are so welcome, I am glad to hear it worked! I do not operate machines but I am fascinated by all of the menu adjustments to support operators so it was a fun challenge. I learned a lot myself