For flanges when welding your own, I always say the thicker the better, the minimum I would use would be 3/8", preferring 1/2" or even 5/8". With these little puppies you can probably get away with less thickness, as long as your bolted on four corners.
I think I should cover anti reversion a little more, just so you know what I'm talking about. In a pipe you never want to expose the gas flow to a step down in the direction of flow - a step like this (i.e. the stock exhaust 1.75" manifold port -> 2" head port exit) is a reflection point for the initial shock waves and following gas pulses. An anti reversion step is a slight step up in diameter in the direction of flow, commonly .030-.050" on the radius. So on a 2" head opening, you would have a 2.06 - 2.1" header port.
You can use a 2" ID 90 bend and cut pies out of the end to step it down to your primary ID size. Use a tailpipe expander to stretch the other opening for the head side, beware that stainless is extremely springy, so it will shrink back some after the expansion each time. Pie-ing the output side and expanding the inlet is how I accomplished this on my header build.
The TWE "oval" on the turbo flange I assume was to fit both turbos without having the port blocked. Unfortunately this scheme will cause that step down effect and in turn a reflection point for the shock waves. Match your flange exactly, or slightly smaller than, the port on the turbo. Avoiding the step down at all costs is generally the best idea.
If you use a proper merge like a Burns, you can step the output, which will invariably be too large, by pie cutting the tubing or by making or buying a premade cone, which is a fairly simple task as well. Again this method is used to avoid that step-down syndrome and reflection point. The Burns and other well-made merge collectors will all have some anti reversion designed into them by thier high angles of attack, which are very difficult for a home welder to do correctly with such precision. Even TWE does not have a tight merge on thier header, although it does look good regardless.
Porting a turbine on a turbo is childs play. I sent my TD04 to deadbolt and almost cried at the cost after seeing the ease of the job, if you've done any porting at all before its about a simple matter as they come. Radius and blend the wheel exit and matching the out flange wasthe extent of the work. Porting the wastegate is another worthwhile mod if you are using an internal wastegate turbo, since technically that will see the majority of airflow at higher rpm - this to prevent creeping. If you are designing for external wastegate, you will notice many good designers will not tack it on as an afterthought, but put it in the direct path of the flow with the turbo as a 'side' exit. Porting the compressor side, my TD04 as done by a shop was just enlarged at the exit. I can take pictures of mine to guide you if you'd like, I still dont have it installed. All 'polishing' is purely cosmetic but people that sell ported things like to make them look good in pictures, and so it has caught on. A mirror finish does not show up on a flow bench, so do whatever you feel like. I leave the cartridge roll finish on everything.
The way I do contructing of tubing systems is a part/section at a time, for tacking I use a proper sized hose clamp and cut a 'window' in it.. . The hose clamp holds the joint perfectly while you tack, rotate and tack, 4 tacks for each joint, then weld. This hose clamp method I learned from a very respectable master of the trade, Ron Covell. Remember to use the Solar flux on the backside of the joints, You can get this from Burns or any number of welding shops that supply for stainless welding. You have to use this if your not using a purge system. Also, there can be no air gap, and I mean none at all, in the joint you are welding on stainless. Take the time and finish the cuts to perfection.
Last thing I'd recommend is to make up a few extra flanges and fix a air adapter on on of them, and pressure test the unit before you do your final install. I tested mine at 50 psi and left it to test for leak down overnight, I made up some gaskets out of gasket material for the test.
The extra mile as I would call it and also would suggest it, is getting some 321 SS sheet and making some heat shielding, I made full wraps where possible and just a curved shield on the inside of bends, etc. Protect the oil pan/oil filter, engine mounts - I just wraped the whole merge collector and under turbo area. Any full wrap heat shielding will keep the heat in better and the surrounding air will be warmer, which can only help spool times. I do not recommend any kind of wrap however. Keep as much of the stock shielding or make your own for above and around the turbo and downpipe too. DP I'm making is 3" with a bell mouth.
4 mounting holes I would say are mandatory. They make the welding less stressful and if you don't have any slipjoints it should keep the expansion of the SS from working the gaskets over. Either way the extra holes are a good investment. I saw Sidewayz used .120 wall, that is very thick for SS. Most systems are 16 guage, .065. The thicker stuff will have more expansion force, I don't even know where to get SS that thick. If you do mild steel, then thickness is a good thing though as the heat retention of mild is far lower. I used 304 for expense purposes for tubing, and 321 sheets for my shields, because I had a cheap source. Remember you can weld SS to mild, which is sometimes done on the turbo flanges to prevent housing cracking, esp. on 4 bolt ones.
Well I think that is enough babble for one post.