I found out how to edit skirmish unit selections. For those who are curious you can adjust "SkirmishUnits_CIS" and SkirmishUnits_Republic" to adjust quantity of a unit available for both lifetime and amount at a single time. Change the "0" in the following lines to your ideal amount:
<Build_Limit_Current_Per_Player>1</Build_Limit_Current_Per_Player>
<Build_Limit_Lifetime_Per_Player>2</Build_Limit_Lifetime_Per_Player>
This limits the amount of the selected unit to 1 at a time, for 2 total per player in a match.
and replace the existing:
<!--<Build_Limit_Current_Per_Player>0</Build_Limit_Current_Per_Player>-->
<!--<Build_Limit_Lifetime_Per_Player>0</Build_Limit_Lifetime_Per_Player>-->

Using the same files I limited the large units that I wanted kept in by adjusting the lines above, in this case for the Lucrehulk Carrier and Secuter.

Now using the "Skirmish_Starbase" file I removed units that I found to be obnoxious in these matches, like all lucrehulks, Subjugators, Praetors, minus hero units and the Carrier (they were kept in but with limited quantity).

Now because the rosters had more space for units (You can have up to 24 units on a roster) I added some things like support Munificents in place of the lucrehulks that were removed, and gave the republic the new Acclamator variants like the Destroyer and Battleship, which are awesome. I did this using the stats provided in "Republic_Space_Units" and added entries to both "SkirmishUnits_CIS" and "SkirmishUnits_Republic" for their respective ships. Simply adding "Skirmish" prior to the name of the units seemed to work when making the new entries.

General file path to access all this looks like: Install location for steam > Steam> Steamapps> workshop> Content> 32470> 1976399102> Data> XML>
"Units" takes you to all of the unit stats and entries.
"Structures" takes you to structures and their available unit selection.

Hope this helps someone looking to clean up their skirmishes.

And for those wanting the entries for "Skirmish_Acclamator_Destroyer" and "Skirmish_Acclamator_Battleship" ill list them here for convenience.

Acclamator Destroyer:

<SkirmishSpaceUnit Name="Skirmish_Acclamator_Destroyer">
<Variant_Of_Existing_Type>Acclamator_Destroyer</Variant_Of_Existing_Type>
<Encyclopedia_Text> TEXT_TOOLTIP_ACCLAMATOR_DESTROYER TEXT_TOOLTIP_SEPARATOR_STAT_BLOCK TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_HULL TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_SHIELD TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_MOVE TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_SQUADRON TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_WEAP1 TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_WEAP2 TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_WEAP3 TEXT_TOOLTIP_ACCLAMATOR_DESTROYER_WEAP4 TEXT_TOOLTIP_SEPARATOR_CAPABILITIES_BLOCK TEXT_TOOLTIP_CAPABILITY_ORBITAL_BOMBARDMENT TEXT_TOOLTIP_CAPABILITY_BOMBING_RUN </Encyclopedia_Text>
<Lua_Script/>
<Tech_Level>99</Tech_Level>
<Space_FOW_Reveal_Range>25000.0</Space_FOW_Reveal_Range>
<No_Colorization_Color> 255, 255, 255, 255 </No_Colorization_Color>
<!-- <MULTIPLAYER SKIRMISH VALUES BEGIN> -->
<Tactical_Build_Cost_Multiplayer>3105</Tactical_Build_Cost_Multiplayer>
<Tactical_Build_Time_Seconds>18</Tactical_Build_Time_Seconds>
<Tactical_Build_Prerequisites>Space_Level_Four_Tech_Upgrade</Tactical_Build_Prerequisites>
<Tactical_Production_Queue>Tactical_Units</Tactical_Production_Queue>
<!-- <Build_Limit_Current_Per_Player>0</Build_Limit_Current_Per_Player> -->
<!-- <Build_Limit_Lifetime_Per_Player>0</Build_Limit_Lifetime_Per_Player> -->
</SkirmishSpaceUnit>


Acclamator Battleship:

<SkirmishSpaceUnit Name="Skirmish_Acclamator_Battleship">
<Variant_Of_Existing_Type>Acclamator_Battleship</Variant_Of_Existing_Type>
<Encyclopedia_Text> TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP TEXT_TOOLTIP_SEPARATOR_STAT_BLOCK TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_HULL TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_SHIELD TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_MOVE TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_SQUADRON TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_WEAP1 TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_WEAP2 TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_WEAP3 TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_WEAP4 TEXT_TOOLTIP_ACCLAMATOR_BATTLESHIP_WEAP5 TEXT_TOOLTIP_SEPARATOR_CAPABILITIES_BLOCK TEXT_TOOLTIP_CAPABILITY_ORBITAL_BOMBARDMENT TEXT_TOOLTIP_CAPABILITY_BOMBING_RUN </Encyclopedia_Text>
<Lua_Script/>
<Tech_Level>99</Tech_Level>
<Space_FOW_Reveal_Range>25000.0</Space_FOW_Reveal_Range>
<No_Colorization_Color> 255, 255, 255, 255 </No_Colorization_Color>
<!-- <MULTIPLAYER SKIRMISH VALUES BEGIN> -->
<Tactical_Build_Cost_Multiplayer>3855</Tactical_Build_Cost_Multiplayer>
<Tactical_Build_Time_Seconds>19</Tactical_Build_Time_Seconds>
<Tactical_Build_Prerequisites>Space_Level_Four_Tech_Upgrade</Tactical_Build_Prerequisites>
<Tactical_Production_Queue>Tactical_Units</Tactical_Production_Queue>
<!-- <Build_Limit_Current_Per_Player>0</Build_Limit_Current_Per_Player> -->
<!-- <Build_Limit_Lifetime_Per_Player>0</Build_Limit_Lifetime_Per_Player> -->
</SkirmishSpaceUnit>

You can copy paste both of these into "SkirmishUnits_Republic.xml", save, and then add "Skirmish_Acclamator_Battleship" and "Skirmish_Acclamator_Destroyer" to the list of unit names underneath your preferred Empire starbase. For example, find:
"<!-- Republic Skirmish Starbases -->"
and search for:
"<Tactical_Buildable_Objects_Multiplayer>"
Underneath this line will be all the available units you can build through the starbase, including upgrades. Simply paste the name of the unit youd like to add, like "Skirmish_Acclamator_Battleship". But make sure the total amount of units doesn't increase beyond 24 total or you'll push the end units off the roster. I removed the early game Pelta, since the Fleet Tender Pelta is unlocked shortly after and the Praetor. Save and enjoy.