Then flex pipe and belt tensioner are suspects.

Rattle on first start after sitting for a few years could be no oil at the top of the engine. Especially if it's not doing the same now after having been started and driven a few times.

If its not the chain its gonna be belt tensioner or one of the pulleys. Its not an exhaust rattle I've diagnosed and fixed a ton of those working at the shop. Its definitely mechanical. Were taking a ride tonight almost 30 min each way so I will report back after that. I'm hoping atleast the hard shifting is going to be gone. I can't imagine not seeing some of the symptoms disappear now that the maf is actually plugged in. Other than the code the only other thing that would make me think air intake problem was that every once I. A while when you start it it will immediately stall out. Then I start again and its fine. Never stalled while driving or at idle. Only when you first start it sometimes.

P0102 causes the hard shifting along with open loop engine operation. Stall after start sound like a dying fuel pump.

Running in open loop makes sense thank you. I'm guessing when I drive tonight I will notice a big difference. I thought maybe fuel filter (if it has one) but because it sat for a year and I've only had it for a week and it hasn't stalled when starting for atleast two days now. Maybe it just needed to be ran after sitting so long. I may be way off but Does it always start in open loop and then use the sensors to achieve a closed loop state? Open loop would kind of be like a choke?

Hard shifts could be related to incorrect transmission mounts, the manual transmission and engine are an inch forward , opposed to the automatic transmission location.
just thinking the differences

Also the evap purge is throwing a code and it takes for ever to fill with gas. I can't help but wonder if that might make it stall when starting sometimes.

A bad upper engine mount can cause noises, look thru the oblong hole in the passenger side inner fender. The head of the tensioner bolt should line up in the middle.

https://cimg1.ibsrv.net/gimg/www.che...e02532bab.jpeg
Like this , if the bolt is lower in the hole , the engine mount is toast!

Thanks that's a great idea I will check that out as well. I really like this car and am hoping to make it last. I'll be leaving in about 30 minutes and we will see if the noise and hard shifting is gone. I will report back. Thanks for the help. I'm glad I joined this site. I'm looking forward to learning from you guys.