Right on, then I'll fire away!
First thing I do when importing the MIDI is make sure everything is timed up properly and synced with the BPM. This is actually the most tedious part since the original Doom MIDI files seem to suffer either a sample rate or metadata issue, because while the tempo information attached may be correct, it is very much out of sync on playback (***not the case with Sigil***). I use Logic Pro X which thankfully has a tool to synchronize the MIDI information with the project tempo by referencing the downbeat on a given track. This can be tricky and isn't always perfect in some cases; for instance, I had to frankenstein "Facing The Spider" with the b-side version of it because the program was getting thrown off by the drum beat (or at least I think that's what was happening). Luckily the b-side version experienced no such issue and was actually correctly synced upon import, though I still had to expand the song to more closely resemble the original.
Once everything is timed properly, I then try to get a feel for which tracks represent their actual counterparts. This is obviously a subjective bit and can take some fussing with just demoing out different sounds until the final sound is reached, but I try to avoid straying too far from what was imported from the source. In the case of say, organs and clavichords, I usually default to synthesizers which I'll sometimes re-amp. In other cases, like for a lot of the bass tracks, I'll layer in a low and heavy metal guitar sound to give those bits more resonance. This actually kind of brings me to my next process....getting the instruments to sound "real".
This part does take some time at first, especially when using just the stock instruments and plugins. Like I mentioned, I use Logic, so that DAW thankfully has some already pretty decent sounding stuff in terms of its samplers and dynamic processors. For both guitar and bass tracks I'll run them through a combination of pedals (light flanger -> distortion), then into an amp simulator and mix that to where it starts sounding heavily distorted yet resonant. I'll also do the usual EQ and compression for those tracks while also sending them out on return tracks using delays and some reverb with EQ on those as well. This next part is kind of weird, but I then duplicate the guitar tracks and change the articulation to a more muted and plucky sound and mix those tracks in with their originals, just enough to provide some attack to the strumming. And if really necessary, I'll manipulate note lengths to give the instruments more sustain.
As for drums, it's kind of a similar process. I use multiple sends and returns with a combination of reverbs, delays, and compression; however, before all of that I use a send to an amp simulator to emulate a sort of re-amp effect. This is typically used at times for a specific drum piece like a snare, but I wanted to completely transform the drums from sounding like it's vanilla out-of-the-box form, so I'd send out the whole kit and top it off with some EQ and a smash compressor. Getting the drums to sound natural, however, really depends on the sampler you're using. The basic one I use happens to have a lot of different percussive sounds per velocity, as well as a wide set of pieces per kit, so I recommend using something similar. If I need to, I'll sometimes layer in another kit with different dynamics and EQ the frequencies I want to fill in the original tracks, but only on rare occasions will I do this (eg. "Dark Halls" and "The Demons From Adrian's Pen").
I try not to use the same settings per say when I approach each project, but this is almost always the default flow I resort to. Hopefully I've provided some insight for your mixes (which I'm curious to hear by the way). If anything was unclear or not thorough enough, please let me know!
. Now, without further ado - 
