Hve,
mame is the only way to go. The computer versions are very inaccurate (especially the Elite 8-bit versions which are nothing like the original). Console ones are better. I had the PC Engine version back in the late 80's - it was very close. All the Sega ones from the 32X version on appear to have been done by emulation, rather than converted, so are pretty much perfect.
No, haven't found the pattern tables in the mame ROMs. You can save many positions in mame (shift-f7) so you can replay things over and over to help see what's going on. I then try and get something similar by entering directions, speed etc. into the data and just trying it out.
Sprites are done from screen captures on mame. then into an art package and colours reduced and object resized. Often then needs quite a bit of manual work for anything with any detail on it. The same with scaling the frames smaller and smaller - lots of manual touching up required as they're too lo-rez to scale well. then into my own utilities (in Access VB!) to convert and write it straight to .atr disk sectors.
I'll help if I can. I haven't looked closely, but it seems to me like Time Pilot enemies don't follow set patterns? They seem to have behaviours rather than just fixed places they go. Maybe they start in a particular spot but it depends what you do as to how they respond? You need to figure out those behaviours. Lots of play on mame!