Found a method that works fairly reliably, of course i didnt massive batch test it to take flaws from the data but it should work fairly well.
All you should need is dosbox (im using 0.65, and none of the other programs like D-fend) and your dosbox.conf file (and the means to edit it)
Before starting, take a moment to make a copy of your original/current dosbox.conf file, rename it and move it somewhere safe, just in case for any reason you have an accident wihle editing it, you can fix it with original.
Instructions (Written in the assumption it is the default settings)
1. Open dosbox.conf with whatever you use to edit it (notepad in my case)
2. Scroll down to the '[cpu]' section, locate 'cycles=3000' and replace '3000' with 'auto'
3. Save the changes and close the file. (If you want, under the '[sdl]' section, 'priority=higher,normal' change it to 'priority=highest,higher' this does help with the loading, but its not gonna help drastically (unless you got a lot of programs running in the background)
4. Start up the game
(during this time, the game may be running at a lot faster pace then you are used to, the mouse will too. try to use the keyboard controls as much as possible)
5. Get to the tower, (if you play in Full Screen, switch to windowed mode for this sequence, as the error box usually kicks you out of Full Screen anyways, and has a tendency to change your screens resolution settings in the process) click or press spacebar to enter, after the lady warrior chick says her spiel, your cdrom should be ejected and you will get the box asking if you want to 'Cancel' 'Try Again' 'Continue'
6. Put appropriate disc in tray, close it, and select 'Try Again'
7. You will get a message saying "The wrong volume is in the drive. Please insert volume (whatever your darkside cd is called) into drive" along with 'Cancel' 'Try Again' 'Continue' ; Select 'Continue'
8. Your computers performance will be the final determining factor at this point. The better it is, the faster the game will load thru to the tower, but rest assured it will load (I usually play at cycle of 8000-10000, it definately took a significantly longer time for the game to load at that rate, but it did load every time i tried it)
9. Save your game, you can now go on playing the Darkside of Xeen's storyline~
(If you of course find the settings unbearable to play in after youre loaded and saved inside the tower, close dosbox, and set the 'cycles=auto' to 'cycles=3000' and if you changed your priorities for this the default setting for it is 'priority=higher,normal'. Also if youre feeling really lazy you can just rename the copy you made to dosbox.conf and overwrite the edited one.)
I truly hope this will help anyone who is stuck at needing to enter Ellsinger's Tower, no matter how far they are in the game (alternatively, I did find out there is an entrance to the tower from the Skyways, which acts in the same manner as using a Pyramid.[/b]