If I understand you correctly, you have a Finale document containing both score and linked parts (inside the very same Finale document) - right?

And you are printing the linked parts (not the score) - right?

What I would suggest:

1) Document menu > Page Format > Parts…

These settings are the default settings for new pages.

Already existing pages are not affected - until you Redefine Pages - as described in step 2) below.

Check that all the Page Format settings are correct for the parts.

If a setting is wrong, then correct it.

Click OK, to exit the Page Format dialog.

2) While viewing the linked part, switch to the Page Layout Tool.

Page Layout menu > Redefine Pages > All Pages of Current Part/Score

This step will update the part with the default settings from step 1) above.

Do the steps 1) and 2) solve your problem?

If you have not done so already, take a look at 

File menu > Page Setup…

Check that the Page Setup settings are correct.

By The Way:

When you print “to a pdf using 2 pages per sheet in landscape”, what PDF software are you using?

Perhaps CutePDF?

Edit Page Margins is not a printer setting, it is a layout tool but will have an effect on how the margins will look, if the following steps are respected.

Do you have the correct values in Document -> Page Format -> Score ?

And in Page Layout, did you select "Redefine Pages (All) to apply these values ?

What are you using for your Windows print driver? Have you tried printing to PDF and fixing it from there? 

I've been using Adobe PDF as the printer...Microsoft Print to PDF doesn't give me the "2 sheets per page" formatting options I need.

I've used "redefine page", I get the same large gap at the bottom. 

… I've used "redefine pages", I get the same large gap at the bottom …

What about

File menu > Page Setup…

?

Are the settings in Page Setup as you need them?

If not, then correct them.

… I've been using Adobe PDF as the printer…Microsoft Print to PDF doesn't give me the "2 sheets per page" formatting options I need …

In Other Words, Adobe PDF gives you the "2 sheets per page" formatting options you need. - right?

Does Adobe PDF also give you the page size you need?

"I've used "redefine page", I get the same large gap at the bottom. "

Is that gap only present on the pdf and in the printed version ? On the monitor, there is no gap ?

If the problem happens with the pdf, you could try to print the pdf with anoother tool : the Graphic Tool of Finale, PDFCreator or CutePDF...