@Adamora, I'm sorry that I don't remember whether your D5000 were brand new when Mark modded them...
But I found some differences in the stock phones when I sneaked a listen here and there in between burning in. Some claim that the effects were very dramatic -- anywhere from 1 hour to 400 hours. To my ears, the changes were subtle. Ultimately I couldn't bear the piercing highs of the stock Denons. Hence the markl mods. I think I had about 200+ hours before sending them off.
Upon receiving the modded D5000, I immediately noted the lack of piercing highs. However, everything seemed a little lifeless. Undaunted, I ran about 8 hours of pink noise through them and sneaked another listen. MUCH BETTER!
I'm probably at 60+ hours right now, and I can't believe how great they sound. No high highs, the mids are lush and the bass is significantly reigned in. I suspect some people may dislike the bass change, but I find it very nice and definitely authoritative with bass-heavy tracks. To quote Radiohead: "Everything in its right place."
As for your tinniness, I would suggest running some pink noise or tunes for a day or two or more.
And for the piercing highs, if the burn in doesn't tame it, I would look at your source and amp. As mentioned, I noticed the highs right off the bat with the stock phones, but not at all with the modded ones. And my Gilmore Lite is known for a slight tilt to highs, so it would have been noticeable immediately. Unfortunately I am not familiar with the iBasso, but I did listen for an hour or so from my iPhone > LOD > Pico, and did not get hit with high highs.
As much as I am not a burn-in voodoo champion, I would suggest you give the D5000 a bit of time. If after a few days (or longer) they don't work for you, see if you can try a different amp and/or source, or maybe the D5000 (modded or not) are not for you.
Whatever happens, good luck!