if adding an extra import section to the PE file is an acceptable option

use tools like iidking and add an import section with all the imports that are resolved dynamically

use add cross referances dialog or idc add_dref() to add cross references to them

code for demo

#include <stdio.h>
#include <windows.h>
#pragma comment(lib , "user32.lib")
DWORD (WINAPI * MyGetShortPathName)(LPCTSTR,LPTSTR,DWORD);
int main (void) {
    MessageBox(NULL,"testing add import" , "Test", MB_OK);
    char modname[MAX_PATH] = {0};
    GetModuleFileName(NULL,modname,MAX_PATH);
    printf("%s\n",modname);
    HMODULE hMod = LoadLibrary("kernel32.dll");
    if(hMod) {
        *(FARPROC *)&MyGetShortPathName = GetProcAddress(hMod,"GetShortPathNameA");
        if(MyGetShortPathName) {
            MyGetShortPathName(modname,modname,MAX_PATH);
            printf("%s\n",modname);
        }
    }
    return 0;
}

compiled and executed

C:\codesnips\addimp\addimp.exe
C:\CODESN~1\addimp\addimp.exe

unmodified imports

00412000  GetCurrentThread                      KERNEL32 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
00412130  MessageBoxA                           USER32   

exe modified with iidking and an import GetShortPathNameA added in the extra import section

C:\codesnips\addimp>fc /b addimp.exe modaddimp.exe
Comparing files addimp.exe and MODADDIMP.EXE
000000E6: 04 05  no of section 
00000131: 90 A0  
00000160: F4 00
00000161: 47 90
00000164: 3C 50
00000278: 00 2E .
00000279: 00 49 I
0000027A: 00 49 I
0000027B: 00 44 D
0000027C: 00 4B K
0000027D: 00 69 I
0000027E: 00 6E N
0000027F: 00 67 G
00000281: 00 02 vsize
00000285: 00 90 
00000286: 00 01
00000289: 00 02
0000028D: 00 5E
0000028E: 00 01
0000029C: 00 20
0000029F: 00 E0

ida imports window copy paste of modified exe

00412000  GetCurrentThread                      KERNEL32 
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
00412130  MessageBoxA                           USER32   
00419058  GetShortPathNameA                     kernel32 

double clicked 419058 -> open view -> open subviews -> crooss referances-> add cross refernces

Up P sub_401000+89 call    ds:GetProcAddress  (data xref)

or idc command

add_dref(0x401089,0x419058,53);
AddCodeXref(0x419058,0x401089,53);