Hi and welcome! Sorry so late responding but have been really busy at work the last couple of days. Sounds like everyone has got you going the right direction too. The search function allows you to find alot of great info and pictures too. Still, feel free to ask questions.
Where are you located? Maybe some one close can lend a hand.
Here is my basic run down on 350 upgrades vs stock stuff cut from previous posts...still have questions, just ask and I'll try to clarify.
Ok, I will chime in and give my 2 cents worth. I have over 15 years of experience messing with the 350s and have have found out (mostly the hard way) what works well for my riding style. I am on a tight military budget so most parts I use are either fabbed or bought used from Ebay. Not everyone will agree on the best mods, or good mods so use whatever you like. These are my personal suggestions and opinions. Nows that's a disclaimer! LOL
1.
Air Box Mods... The factory airbox, snorkel and tail light box. Great for keeping out dirt, mud, rain ect., but extremely air flow restrictive especially in hopped up machines where you need increased air flow. There are alot of posted pictures of snorkel mods, each a little different and all fix the restrictive problem. Probably best bang for the $15 spent! Avoid any type of "Ram Air" or scoop mod, the air being forced into system will make jetting a nightmare. The
Engine WILL pull what it needs with the fore mentioned snorkel mod.
2.
Air Filters. Hot debate topic with different views, all require proper oiling and regular cleanings, especially in a dusty environments. A pair of oiled K&N filters with prechargers on a dual snorkel mod with the dual layered oiled foam filter in the box is the best/safest filtering that can be done with excellent air flow, in my opinion.
Factory foam filter(In box) --probably the best filtering but most restrictive because its a very dense type of foam filter over a metal screen cage inside.
Dual stage, Uni foam filters--most commonly used, great flow and good filtration.
K&N filters-- most air flow but least filtering even with the optional outer precharger covers. most expensive also.
pod filters(No box)--again, debatable, you may lose power by removing the box because of the two stroke pulsewave/resonance, loosing the box makes access to the carb much easier, the filter is exposed the elements and needs to be covered when not in use, generally does not like water covered trails!
3.
Carbs--again 32mm(stock)is too small for hopped up engines but fine for stockers. If you want your Engine for torque(hard launches, steep climbing, ect) stay small 34-36MM, if you want your Engine to rev high and really pull on top end, ie duning, go big 38MM,39MM,41MM. Of course you will want your port job, larger or smaller carb, reeds, and your exhaust pipe to all be matched to the setup you want to run...high rev or torque.
The more modern flat slide type carbs (PJ, PWK, quadvent(Airstryker), TMX(Mikuni),etc, give a better throttle response than the stock type round slide carbs(PE). I prefer Keihin over Mikuni,mainly because the 350 choke and throttle cables hook up without having to buy adaptors or new cables...and I am used to the jet size numbers.
4.
Exhaust pipes-- Stock works well and is the quietest but is restrictive when hopped up. DG, PowerPros and Bills are some that I have tried, and all give good gains. The DG silencer(or lack there of) is horribly loud and has to be swapped out ASAP, generally with a long FMF large CC 2 stroke quad/bike silencer. Turbine 2 cores are a popular choice. Again, some have been tuned/designed for rev or torque.
5.
Reeds--Stock are steel and very trust worthy but restrictive on built engines. Boysene makes replacement fiberglass reed pedals for the stock cage in either rev or torque pretty cheap. Also most 250R, CR250, TRX250, ATC250R and pilot reed cages will fit in the 350. I personally prefer the 4 pedal cages(best flow). I also have used a straightened neck boysene Rad Valve, G-3(Mossbarger 8 petal), ESR, Boysene fiberglass on stock cage, and Delta V Force reeds, all with increased power and throttle response over stockers. There has been some verified cases of the V force cage getting sucked into the engines. I don't recall if they were version 1,2, or 3. I have used the 2nd version for years with no problems, yet. Knock on wood. Reeds do not generally make huge power differences, just smooth out a power band, IMHO.
6.
Clutches--Again another topic of debate, all require proper cleaning and lube occasionally for proper operation and long clutch life
--- Salisburys(stock) good ol reliable but a lower engagement bogs the Engine for racing but perfect for kids or general puttering around.
---94C-great all round clutch, draw backs are its not easily tunable, but parts can be changed. Most popular swap if you just want to replace the stock unit.
---102C- great for racing because you can adjust engagement and different areas of the powerband by changing springs or cam arms. Draw backs-expensive, without the dustcover can wear parts quickly.
---HRD & Alt--good simple design clutch(very similar to the 94C) except you can adjust puck weights for tuning easier, priced between the 102 and 94. Drawbacks tends to tear up the "D" slot on the cover and possibly has ties to Pilot main bearing failures, none know damage on 350s yet.
7.
Porting-- The heart and sole of the Engine, can be mild to full race(wild). If not done correctly, you can ruin an Engine. It needs to be done by a knowledgeable person, not a shade tree(like me). You can take a dremel and clean up casting flaws and other imperfections inside the jug, polish up the exhaust port and make better flow thru the Engine(better power) but avoid changing the size and shape of the openings. That is the timing and could spell disaster if you do it wrong. There are alot of articles written on porting work so if you want to do it, better do the homework...or send to a reputable place such as EEE and not a shady type lurking about(no names, just ask).
8.
The little tricks-- here are just a few I use.
--- The stock head gasket is actually three layers. I use only 1 which bumps up the compression some.
---Always use a quailty synthetic oil at 40 or 32:1 with fresh premium gas.
--- Run a liq cooled head and radiator to help control heat especially with a built up Engine.
--- I use an EGT and a water temp gauge to help monitor things.
---Run .190 aluminum rims and lighter weight tires if not in rough/rocky areas, less kenetic mass which allows more power to reach the ground.
---Putting you rubber manifolds and curved airbox to carb rubber boot in boiling water for a short period will aid in attaching them to a larger carb.
---When your cylinder needs the next bore, go to the next size up, do not jump straight to the max bore(82MM). 2 strokes need flow to make big power. Power increase from 78.5MM to 82MM would be very minimal and when that bore is done, you will need to replace the sleeve(expensive).
---Be sure to have the exhaust bridge relieved and cooling holes drilled on the piston during rebuild time. Don't forget to smooth out all ports and transfers edges after a bore job. Hoser(website owner) will bore your cylinder for free, doesn't get any better than that! Huge "Thank You" for helping out the board members and keeping these great machines alive and kicking.
---Do a leakdown test at least annually or after a long vacation of riding. That shouldl catch seals going bad before your Engine leans out and seizes.
---early CR250 mossbarger/elsinore bikes(78/79) used a straight intake manifold and works well for increased flow and larger carbs.
---I do a compression check after every trip and keep it in a log so I know approximate hrs and notice changes in compression(long term ring/cylinder wear)
---If rebuilding with a Honda(Art) piston (78.5-79.5), bore .003, if rebuilding with a Wiesco piston(80-82mm), bore .004-.005 with liq cooling and .005 air cooling. That is due to piston material content and the Wiesco expand more, not the .003 they claim. Trust me, been there done that too many times. Wiesco also claims you should replace the piston after every 20 hrs of run time, or some crummy disclaimer crap like that. They are not bad pistons when run properly.
There is a good start of info to absorb and I am sure other will add to the list too. I am sure I have forgot things too. Good luck,
Gary