I went to the download site. The following is what the site shows. Numbers 1, 2, 3, 4 are the main mod. All others are optional. Did you install with JSGME in order 1 2 3 and 4? Did you allow for overwriting when the prompts told you? If yes, I have no other reason why you are having theses problems except a bad download.
1. NYGM_Tonnage_War_V2.5_Full_Version.7z (Essential, 322 MBytes)
2. NYGM3_New.7z (Essential, 102 MBytes)
3. NYGM3_6F.7z (Essential, 58 MBytes)
4. NYGM_2017A.7z (Essential, 14 MBytes)
5. IABLShipsforNYGM_New_Thomsen.7z (Optional, 14 MBytes. UPDATED VERSION March 2017 for NYGM_2017A.)
6. 3rd Flotilla Mod.7z (Optional, 60 KBytes)
7. SH3_Commander_Updates_for_NYGM.7z (Optional, 0.07 MByte)
8. MFM-Interim-Beta_NYGM.7z (Optional, 35 KBytes)
9. Stiebler4C_V16B1.7z (Optional, an upgrade of the 3A variant but more complex to install; 22 MBytes; includes many new turms for radar.)
10. EnvSimAct_10.7z (Optional, 5 KBytes)
11. NYGM_HiRes_Submarines_3_6F.7z (Optional, 104 MBytes - please observe large size to download)
12. WYGM.7z (Optional, 35 MBytes)
13. Hsie/Stiebler Options Selector (Optional, 157Kbytes)
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