Hi Snoopytheace and welcome to the forums.
I don't use the MD-88, but I can help you with the 727.
First of all, delete the aircraft from FSX-SE and we will start again.
Now, make sure you have downloaded the "JT8D-17 LEAPS/NTL" base pack from the HJG website. Unzip and install the folder "HJG Boeing 727-200 adv LEAPS NTL JT8D-17 v2.0" into your "SimObjects\Airplanes" folder.
Next, delete the "Aircraft.cfg" file as this one is designed for FS2004. Now rename the "Aircraft_FSX.cfg" file to "Aircraft.cfg"
Once that is done, unzip your downloaded repaint of the TWA1998 repaint (b727-200advc_twa_1998_231advc_n54340) and place it into the "HJG Boeing 727-200 adv LEAPS NTL JT8D-17 v2.0" folder in FSX (SimObjects\Airplanes)
On the HJG website, find the picture of the aircraft next to the download link and right click, save as. Go to the pic and change the name to Thumbnail.jpg
Now copy the "thumbnail.jpg" pic to the file you just copied (b727-200advc_twa_1998_231advc_n54340) in FSX.
Go back to the download of the base pack "JT8D-17 LEAPS/NTL" and you will se a folder "Additional Textures B727-200", open the folder and copy the two .bmp files and paste them into the "b727-200advc_twa_1998_231advc_n54340" texture folder in FSX clicking overwrite original files if asked.
Open the "Add to aircraft text" and select all and copy.
Now go back to the FSX and open the "Aircraft.cfg" file. If it wont let you open it, right mouse click on the file and click on "open with" and then select "Notepad".
Once it is open, go to the gap after;
//B727-200 ADV P&W JT8D-17 LEAPS NTL (Leading Edge Adavanced Performance no tail light configuration) V2
//Use HJG supplied B727-200 ADVANCED LEAPS QW2 V2 panel (only) with this aircraft base pack
//FSX
//Add your [fltsim.xx] sections here.
//Remember to start with 0 (zero).
//Copyright Historic Jetliners Group. No uploading to any website without prior approval.
//March 2014
and then paste the info you save from the "Add to aircraft text" file.
Here are the important bits......
On the data you just pasted, change where it says [fltsim.X] to [fltsim.0]
Find where it says "Model=" and change it to Model=NTL
Next, scroll down to "ui_variation=TWA (1998)" and on the next line add the following ui_createdby="HJG"
Save and close the file.
Start up fsx. click on select aircraft and make sure that you have ticked the box "Show all variations".
Click the "All" button under "Publisher" and scroll down to HJG. If you have followed the above, the aircraft should be there.
Remember,
1:make sure you are using the right base pack.
2:Delete the aircraft.cfg and rename the aircraft_fsx.cfg to aircraft.cfg
3:Copy the little thumbnail picture of the plane from the HJG Website and rename it to thumbnail.jpg
4:Copy the texture file and add the thumbnail.jpg pic to it.
5:Copy the two .bmp files from Additional Textures B727-200 into the b727-200advc_twa_1998_231advc_n54340 folder.
6:Add the following to the aircraft.cfg
[fltsim.0] // Change "xx" to next number in sequence starting from 0
title=Vistaliners Boeing 727-200 ADVC TWA 1998
sim=B727200ADVC_VL
model=NTL
panel=
sound=
texture=twa_1998_231advc_n54340
atc_id=N54340
atc_heavy=0
atc_flight_number=722
atc_airline=TRANS WORLD
atc_parking_codes=TWA
atc_parking_types=GATE,CARGO,RAMP
ui_manufacturer=Boeing
ui_type=727-200 ADVC
ui_variation=TWA (1998)
ui_createdby="HJG"
description=One of the most successful commercial jet airliners ever designed. Production totaled 1,831 aircraft between 1963 and 1984. \n\n Repaint by Frank IDONE & Camilo LUENGAS
visual_damage=1
atc_id_color=0x00000000
atc_id_font=Verdana,-11,1,600,0
Making the changes highlighted in red and save.
7: Start FSX and ensure that "show all variations" is ticked in the select aircraft menu.
Hope this has been of some help,
Cheers,
Nathan