How clean is clean? Some parts of the engine, such as the apex and side seal grooves, need to be as clean and free of carbon buildup as possible to get the best performance out of the engine. Other areas, such as the outsides of the housings, only need to be as clean as you want them to be. Still, it's hard to inspect the engine parts properly without cleaning them, so unless you see obvious signs of damage you should do this step first.

Essential materials for the cleaning job include:

• Razor blades
• Broken pieces of side seals - save these during disassembly!
• An assortment of dental picks
• Brass-bristled wire brushes
• 180-grit aluminum oxide and 400-grit silicon carbide wet-or-dry sanding discs
• Kerosene

These items are not essential, but I found them to be very handy:

The first is exactly what it looks like - a plastic kiddie wading pool, the hard-sided style, not inflatable. These are cheap at any dime store, and you can even get them for free at tag sales. Dirty and cracked is fine, as long as the bottom is relatively sound.

When you crack open your core all KINDS of stuff is going to fall out. A lot of it will be motor oil and coolant, with carbon and other junk mixed in. I also had plenty of varnish solids from dried-up gasoline to play with. Then you're going to douse the pieces with carb cleaner and attack it with wire brushes, all while trying to not lose important bolts and other parst. A professional mechanic will have a parts washer. If you don't, this works almost as well, keeps the junk off your shop/garage floor, and is easy to clean up and store when you're done.

The second gem is an ultrasonic cleaner - I found a good price on a barely-used unit on eBay. If you can't find one for a good price, no big deal. But if you CAN, it will work wonders on cleaning old junk off your parts. Sandblasting also works, but this cleaner can clean an entire part, even inside things like intake runners and water cooling jackets. For irons and rotor housings, I just put them in on two cycles, one for each half (only half will fit in the tank at a time).

It's easy to clean the outside of a side housing - spray it with carb cleaner (I like the foaming kind for dealing with heavy buildup), let it soak in, then go at it with a brass-bristled wire brush. If you have a parts washer you can do the job faster, but since I didn't have one I found a cheap Rubbermaid bin worked great. I could clean up the parts, keep all the muck together, then seal it up when I was done.

Examine the O-ring grooves carefully. It's very easy to miss small pieces of O-ring or sealant in the grooves. Run a razor blade, dental pick, or side seal along each groove to make sure it's completely clean and free of debris. You should also inspect the water jacket holes for debris and buildup. It's normal to have some accumulated sediment in here, and not a necessity to remove it all. But excessive sediment buildup may indicate that the engine went through some trauma (contaminants in the coolant, blow-by from failing water jacket O-rings due to overheating the engine, etc), so keep an eye out for it.

When you're done you can send the housings to be lapped to produce a gorgeous new finish. Or not - provided your wear (see Inspection) is within limits, lapping isn't necessary. Or you can do something similar by hand in just a few minutes. Lynn E. Hanover describes the following technique that he uses to break the surface glaze and promote side seal seating:

There should be no attempt to reduce the surface enough to remove the wear marks
(Groove along the plugs side of the iron). This groove is caused by hot metal
wearing more quickly than cooler iron. So, the groove forms from the side seal
moving in a somewhat vertical path. The same exact wear would occur on the opposite
side but for the cooler iron. Right? The wear limit of this groove depth is .004".
It can be removed by grinding and lapping. That is reducing the entire surface
exactly the same amount. Or just lapping for a very long time. Either operation is
acceptable. The irons should be renitrided after either process.

One light lapping probably would leave a nitrided layer since it starts out at about
.003" deep. This is for street engines that do not get disassembled often. It makes
no difference in a race engine.

You hone a piston engine cylinder to remove the glaze. That is the chrome like
finish of the bore walls caused by the rings wearing away some of the surface. New
rings installed in a slick chrome like bore will take years to break in. The oil
scraper ring will remove all oil from the bore on each stroke and the new rings will
spoil from over heating.

Same thing in the rotary. To remove the glaze. The shiny surface, and replace it with
a rough surface that will hold a supply of oil to help lubricate the side seals. The
side seals are the piston rings of the rotary.

The object here is to remove the glaze with the rather course 180 grit paper on the
random obital sander. A air powered 5" round aluminum oxide disc is what I use, but an
electric unit would be fine. I run the disc dead flat on the iron long enough to
remove all of the staining done by water in the seal grooves. Go real light on the
legs. Material comes off real fast with high unit pressures, Then a fancy lapping
session or glue some wet or dry silicone carbide 400 grit paper to an old disc pad,
and wet the iron with kerosine and run over it again nice and flat just long enough to
get a flat grey look to it. About 5 minutes, and keep it wet. A new dry 180 grit disc
and a new silicone carbide disc for each iron face. You can do the wet part in the
cleaning tank for less mass making.

Then off to the car wash for a long wash and wrinse. Then dry with old clean towels
and spray with WD-40. Now you have a finish that will last through several rebuilds.
Provide quick break-in, and long life and high compression form the side seals and
corner seals. The swirl marks from the 180 grit will outlast the irons.

Just don't use a synthetic oil in a fresh rebuild. Run a few hours with dino oil, then
dump it and change filters, and run what you want. If the OMP is in use, a good brand
of dino oil and if you premix, a synthetic racing oil in the sump. 

You don't have to do this step, but it does make for better seal break-in, it's fast, and it's easy. Here are some photos of the results:

Rotors often get the worst of it in terms of carbon buildup, which can be very hard to remove. Sure, you can soak them in oven or carb cleaner and have at it with brass-bristled brushes… OR you could use the method depicted by Pineapple Racing below and get the job done in just a few minutes:

I would advise against disassembling the oil pump. If it's damaged the damage will almost certainly be visible under careful inspection, and a new unit would be a fast and cost-effective alternative to rebuilding it.

To clean it, just wipe it down with a lint-free rag, then re-lubricate it with clean engine oil. Don't worry about doing a perfect job. A quarter ounce of dirty oil from the old engine isn't going to hurt anything. Remember, you're going to change the oil after just a few hours anyway, to inspect it for early warnings of problems.

Inspect the oil pan carefully for any signs of damage. Some engine importers drag the engines around on their pans, so they can be dented and even punctured. A few small dents are fine, but significant damage may justify the purchase of a new pan.

If you can reuse the pan you have, Simple Green makes an easy and fast cleaner. Spray it in, wait a bit, then pour it out. Repeat once or twice, then rinse with clean water and dry thoroughly. Spray it down with WD-40 to protect it from rust until you're ready to use it.