I can't actually TAS this -- I don't have a Windows machine to run the emulator on -- but I thought it'd be worth starting a thread; I have some thoughts on planning.
First off, obviously play on hard. Enemies are more aggressive, shots move faster; it's not just a matter of enemies having more hitpoints.
It's tricky to say what S Bonuses should be taken. At first I'd say "don't get the ones that take longer", but there's the stage 6 boss to consider - you get a sort of secret boss if you kill it the right way (and that's part of getting the last S Bonus on the level). However, most of them don't involve anything that looks particularly special, so I'd have to say avoid e.g. killing the bottom half of the Greive (assuming the alternate path is longer than the normal path, which I think it is), or trying to get lots of turret kills in stage 2.
This FAQ has a list of all of the S Bonuses; I'd suggest skipping 1-3, 2-2, 2-3, 3-2, possibly 4-1, 5-2, 6-1, and 6-2. That gets 13 S Bonuses, annoyingly not enough to unlock Unknown Fighter 1 according to the FAQs (but you'll be unlocking Unknown Fighter 2 regardless, so that's all good).
As far as ship choice, I think the best bet is to go for the Astraea. Reason being that it can bring the most power to bear at any given time; it's hard to beat a Grenade/Cannon combo for DPS, for example. Secondarily, since you get more points and a higher bonus gauge boost for killing with gunpods, the Astraea is the clear winner for racking up high scores. It does make planning a bit harder, though, since you frequently won't have a machinegun handy to kill the mooks.
Your firing rate is limited by how quickly your shots either hit something or go offscreen. Each weapon (including the machinegun) has a certain number of onscreen shots at a time - get in close so that you firing rate isn't throttled down. For example, the Spreader can have one spread onscreen at a time, but it has very little cooldown between shots. This means you can turbo-fire it if you get into the target's face so all five bullets hit. I don't know exactly how much potential damage a Spreader pod has compared to the others, but its DPS should be excellent. Grenades, similarly, can have two shots onscreen; Cannons, one. The Blade deals continuous damage; it's pretty powerful, but I don't think it compares to other weapons which are normally limited by their firing rate. The Riot has hideous cooldown; I can't see using it for anything beyond demonstration purposes.
I haven't done any scientific investigation into DPS, but here's my guess at rankings:
Grenade
Flash
Spreader
Hedgehog
Cannon
Juno
Blade
Wasp
Riot
Vulcan
No idea where the Mosquito and Python/Ptyhon fit in there. The Cannon and Juno are both rather limited by their maximum firing rate; ordinarily they're good because the individual shots are powerful and easier to land hits with.
The big problem I see with boss-killing is that some of the weapons have awkward firing angles. It could be difficult to maximize your damage potential with the Grenade while still landing relevant hits with the other gunpod, for example.
This video shows someone playing through stage 5 without firing a shot. This is mostly notable for the use of the manipulator to kill enemies and bosses - they die with impressively few hits. I believe the manipulator is "armor-piercing" much like the Riot. It also can be used to block bullets. Most of the time you should have both gunpod slots full, which means no manipulator, but when you do, it's worth kicking a few things. The manipulator also, of course, gives you a way to hit things behind you when you don't have a Spreader or Grenade handy. I know I've used this on stage 2 for killing some of the robot arms on the left side of the screen. Finally, note that you can hurt things by changing your speed. Naturally.
When you can, kill enemies in interesting ways. For example, taking out enemy engines causes them to crash. The boats in the first half of stage 4 can be flipped by firing a cannon underwater. The "dangling" enemies in stage 4 (and the cannon turrets in 4) can be made to flip about uselessly if you kill off their armaments. Fortunately, the game seems to be lag-free, so you should be able to play with your pals before blowing them up.
I don't know that there's much of a difference, gameplay-wise, between the English and Japanese versions. The Japanese version has a level-select mode which might be useful for testing things, though. Fortunately all the dialogue is in German. :)
(It is really weird seeing a window that has OSX-style window bars but Windows-style widgets)
Edit: the CD-ROM issue might have something to do with Crossover not exposing the CD-ROM drive to the program; I'm not at all certain, though.